Available Software for Swan

HCC provides some software packages via the Apptainer container software. If you do not see a desired package in the module list below, please check the Using Apptainer page for the software list there.

Module prerequisites

If a module lists one or more prerequisites, the prerequisite module(s) must be loaded before or along with, that module.

For example, the cdo/2.1 modules requires compiler/pgi/13. To load the cdo module, doing either

module load compiler/pgi/13

module load cdo/2.1

or

module load compiler/pgi/13 cdo/2.1 (Note the prerequisite module must be first.)

is acceptable.

Multiple versions

Some packages list multiple compilers for prerequisites. This means that the package has been built with each version of the compilers listed.

Custom GPU Anaconda Environment

If you are using custom GPU Anaconda Environment, the only module you need to load is anaconda:

module load anaconda

last generated 2024-10-11T05:03:34CDT

Name Version Module Name Prerequisites Type Domain Description
3d-dna 201008 3d-dna/201008 None application computational biology 3D de novo assembly (3D-DNA) pipeline.
3dslicer 4.11.20210226 3dslicer/4.11.20210226 None application biomedicine 3D Slicer is a free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research.
BICseq 1.1.2 BICseq/1.1 None application computational biology BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion.
CNVnator 0.4.1 CNVnator/0.4 None application genotyping CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
GSL 2.6 GSL/2.6 compiler/pgi/20 compiler/intel/19 compiler/gcc/11 compiler/intel/20 compiler/gcc/10 library runtime support
LIS 7.3 LIS/7.3 compiler/intel/19:openmpi/4.0 application Simulation
MEME 4.11.2 MEME/4.11 compiler/gcc/11:openmpi/4.1 application computational biology The MEME suite is a collection of tools for the discovery and analysis of sequence motifs. It is hosted at http://meme-suite.org/.
MEME 5.5.5 MEME/5.5 compiler/gcc/11:openmpi/4.1 application computational biology The MEME suite is a collection of tools for the discovery and analysis of sequence motifs. It is hosted at http://meme-suite.org/.
NCL 6.1 NCL/6.1 None application utility NCAR Command Language
NCL 6.3 NCL/6.3 None application utility NCAR Command Language
NCL 6.4 NCL/6.4 None application utility NCAR Command Language
NCL 6.6.2 NCL/6.6 None application utility NCAR Command Language
NCO 4.9.4 NCO/4.9 compiler/pgi/20 library runtime support
NCO 4.9.9 NCO/4.9 compiler/intel/20 library runtime support
NUWRF v9 NUWRF/intel/v9 None library runtime support
R 3.4.4 R/3.4 None library runtime support R is a free software environment for statistical computing and graphics.
R 3.5.1 R/3.5 None library runtime support R is a free software environment for statistical computing and graphics.
R 3.6.3 R/3.6 None library runtime support R is a free software environment for statistical computing and graphics.
R 4.0.5 R/4.0 None library runtime support R is a free software environment for statistical computing and graphics.
R 4.1.3 R/4.1 None library runtime support R is a free software environment for statistical computing and graphics.
R 4.2.2 R/4.2 None library runtime support R is a free software environment for statistical computing and graphics.
R 4.3.3 R/4.3 None library runtime support R is a free software environment for statistical computing and graphics.
RAPSearch2 2.19 RAPSearch2/2.19 None application computational biology RAPSearch2 is a tool for fast protein similarity searches.
SRAtoolkit 2.10.0 SRAtoolkit/2.10 None application computational biology SRA Toolkit and SDK from NCBI
SRAtoolkit 2.11.0 SRAtoolkit/2.11 None application computational biology SRA Toolkit and SDK from NCBI
SRAtoolkit 2.8.2 SRAtoolkit/2.8 None application computational biology SRA Toolkit and SDK from NCBI
SRAtoolkit 2.9.6 SRAtoolkit/2.9 None application computational biology SRA Toolkit and SDK from NCBI
StringTie 1.3.0 StringTie/1.3 None application computational biology StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
StringTie 2.1.2 StringTie/2.1 None application computational biology StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
StringTie 2.2.1 StringTie/2.2 None application computational biology StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
TrimGalore 0.4.5 TrimGalore/0.4 None library runtime support
WRF v3 WRF/v3 compiler/pgi/20:openmpi/4.0 library runtime support
WRF v4 WRF/v4 compiler/intel/20:openmpi/4.0 compiler/pgi/20:openmpi/4.0 library runtime support
abacas 1.3.1 abacas/1.3 None application computational biology ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
abaqus 2021 abaqus/2021 None application Engineering Abaqus is a software suite for finite element analysis and computer-aided engineering.
abayesqr 1.0 abayesqr/1.0 None application high-throughput sequencing data aBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data.
abinit 9.6.2 abinit/9.6 compiler/gcc/10:openmpi/4.1 application Physics ABINIT is an atomic-scale simulation software suite.
abricate 0.8.13 abricate/0.8 None application Biology Mass screening of contigs for antibiotic resistance genes
abricate 1.0.1 abricate/1.0 None application Biology Mass screening of contigs for antibiotic resistance genes
adfr-suite 1.0 adfr-suite/1.0 None application Chemistry AutoDockFR (or ADFR in short) is a protein-ligand docking program developed in the Sanner laboratory at Scripps Research under the AutoDock umbrella
admixtools 7.0.2 admixtools/7.0 None application admixture ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
afni 18.2.06 afni/18.2 None application MRI AFNI is a suite of programs for looking at and analyzing 3D brain images.
afni 21.1.06 afni/21.1 None application MRI AFNI is a suite of programs for looking at and analyzing 3D brain images.
afni 22.0.21 afni/22.0 None application MRI AFNI is a suite of programs for looking at and analyzing 3D brain images.
afni 23.1.10 afni/23.1 None application MRI AFNI is a suite of programs for looking at and analyzing 3D brain images.
afq a42e157 afq/a42e157 None application matlab toolbox Automated Fiber Quantification.
afq c59f21b afq/c59f21b None application matlab toolbox Automated Fiber Quantification.
afterqc 0.9.6 afterqc/0.9 None application package Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats.
agat 0.9.2 agat/0.9 None application bioinformatics Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
agfusion 1.0 agfusion/1.0 None application Biology AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
agfusion 1.251 agfusion/1.251 None application Biology AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
aligngraph 1.0 aligngraph/1.0 None application computational biology
allinea 18.0 allinea/18.0 None application Utility
allinea 18.2 allinea/18.2 None application Utility
allinea 19.0 allinea/19.0 None application Utility
allinea 21.0 allinea/21.0 None application Utility
allinea 22.0 allinea/22.0 None application Utility
allinea 22.1 allinea/22.1 None application Utility
allinea 4.2 allinea/4.2 None application Utility
allinea 5.0 allinea/5.0 None application Utility
allinea 5.1 allinea/5.1 None application Utility
allinea 6.0 allinea/6.0 None application Utility
allinea 6.1 allinea/6.1 None application Utility
allinea 7.0 allinea/7.0 None application Utility
ambertools 22 ambertools/22 compiler/gcc/10:openmpi/4.1 application computational chemistry
ambertools 23 ambertools/23 compiler/gcc/11:openmpi/4.1 compiler/gcc/10:openmpi/4.1 application computational chemistry
ambertools 24 ambertools/24 compiler/gcc/10:openmpi/4.1 compiler/gcc/11:openmpi/4.1 application computational chemistry
amorph 2021.05.10 amorph/2021.05.10 None application environment AMORPH utilizes a new Bayesian statistical approach to interpreting X-ray diffraction results of samples with both crystalline and amorphous components.
amos 3.1.0 amos/3.1 None application computational biology A Modular, Open-Source whole genome assembler
anaconda 2.7 anaconda/2.7 None application system
anaconda 23.1.0/1.3.1 anaconda/23.1 None application system
anaconda 23.11.0/1.5.4 anaconda/23.11 None application system
anaconda 23.7.2/1.4.9 anaconda/23.7 None application system
anaconda 3.3 anaconda/3.3 None application system
anaconda 3.4 anaconda/3.4 None application system
anaconda 4.10.3 anaconda/4.10 None application system
anaconda 4.12.0/0.24.0 anaconda/4.12 None application system
anaconda 4.3 anaconda/4.3 None application system
anaconda 4.6 anaconda/4.6 None application system
anaconda 4.8 anaconda/4.8 None application system
anaconda 4.9.2 anaconda/4.9 None application system
angsd 0.935 angsd/0.935 None application Bioinformatics ANGSD: Analysis of next generation Sequencing Data
angsd 0.937 angsd/0.937 None application Bioinformatics ANGSD: Analysis of next generation Sequencing Data
ansys 19.2 ansys/19.2 None application Engineering ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires.
ansys 2021R2 ansys/2021 None application Engineering ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires.
ant 1.10.1 ant/1.10 None library java Java build tool
ant 1.9.9 ant/1.9 None library java Java build tool
antismash 6.1.0 antismash/6.1 None application Biology antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
ants 2.5.1 ants/2.5 None application computational neuroimaging ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.
anvio 6.1 anvio/6.1 None application Omics A platform for integrated multi-omics
anvio 6.2 anvio/6.2 None application Omics A platform for integrated multi-omics
anvio 7 anvio/7 None application Omics A platform for integrated multi-omics
anvio 7.1 anvio/7.1 None application Omics A platform for integrated multi-omics
apkid 1.0.0 apkid/1.0 None application Malware APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android.
apptainer 1.1 apptainer/1.1 None application system Application containers enabling mobility of compute.
aria2 1.23.0 aria2/1.23 None application tool aria2 is a lightweight multi-protocol & multi-source command-line download utility.
aria2 1.34.0 aria2/1.34 None application tool aria2 is a lightweight multi-protocol & multi-source command-line download utility.
aria2 1.36.0 aria2/1.36 None application tool aria2 is a lightweight multi-protocol & multi-source command-line download utility.
aria2 1.37.0 aria2/1.37 None application tool aria2 is a lightweight multi-protocol & multi-source command-line download utility.
arpack-ng 3.9.1 arpack-ng/3.9 compiler/intel/20:openmpi/4.1 library runtime support
arriba 2.4.0 arriba/2.4 None application computational biology Fast and accurate gene fusion detection from RNA-Seq data
art 2.6.0 art/2.6 None application computational biology ART is a set of simulation tools to generate synthetic next-generation sequencing reads.
ase 3.18.1 ase/3.18 None application Physics ASE is a python package providing an open source Atomic Simulation Environment in the Python language.
ashs 1.0.0 ashs/1.0 None application MRI ASHS is software for automatic segmentation of the medial temporal lobe (MTL) substructures from brain MRI scans.
ashs 2.0.0 ashs/2.0 None application MRI ASHS is software for automatic segmentation of the medial temporal lobe (MTL) substructures from brain MRI scans.
aspera-cli 3.7.7 aspera-cli/3.7 None application system IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.
aspera-cli 4.14.0 aspera-cli/4.14 None application system IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.
asreml 3.0 asreml/3.0 None application data analysis ASReml
asreml 4.1 asreml/4.1 None application data analysis ASReml
asreml 4.2 asreml/4.2 None application data analysis ASReml
atat 3.36 atat/3.36 compiler/gcc/11 application Chemistry
atk 2016.3 atk/2016.3 None application Chemistry
atomate2 0.0.10 atomate2/py38/0.0.10 None application Simulation atomate2 is a library of materials science workflows
atomate2 0.0.10 atomate2/py39/0.0.10 None application Simulation atomate2 is a library of materials science workflows
atomate2 0.0.10 atomate2/py310/0.0.10 None application Simulation atomate2 is a library of materials science workflows
augur 12.0.0 augur/12.0 None application public health Process pathogen genome data for the Nextstrain platform
augustus 3.0 augustus/3.0 None application computational biology AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus 3.2.3 augustus/3.2 None application computational biology AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus 3.3 augustus/3.3 None application computational biology AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus 3.4 augustus/3.4 None application computational biology AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus 3.5.0 augustus/3.5 None application computational biology AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
autoconf 1.0 autoconf/2.69 None application Utilities The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
autodock 4.2.6 autodock/4.2 None application Chemistry AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
autodock-gpu 1.2 autodock-gpu/1.2 None application Chemistry AutoDock for GPUs using CUDA.
autodock-gpu 1.3 autodock-gpu/1.3 None application Chemistry AutoDock for GPUs using CUDA.
autodock-gpu 1.4.3 autodock-gpu/1.4 None application Chemistry AutoDock for GPUs using CUDA.
autodock-gpu 1.5.3 autodock-gpu/1.5 None application Chemistry AutoDock for GPUs using CUDA.
autodock-gpu 2024.03.05 autodock-gpu/2024.03.05 None application Chemistry AutoDock for GPUs using CUDA.
autodock-gpu 4.2.6.c135512 autodock-gpu/4.2 None application Chemistry AutoDock for GPUs using CUDA.
autodock-vina 1.1.2 autodock-vina/1.1 None application Chemistry AutoDock Vina is an open-source program for doing molecular docking
automake 1.0 automake/1.16 None application Utilities The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
autotools 1.0 autotools/1.0 None application Utilities The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
awscli 1.1.120 awscli/1.11 None application utility Universal Command Line Environment for AWS.
awscli 1.19.5 awscli/1.19 None application utility Universal Command Line Environment for AWS.
awscli 1.23.6 awscli/1.23 None application utility Universal Command Line Environment for AWS.
azcopy 7.2.0 azcopy/7.2 None application Utility AzCopy is a command-line utility designed for copying data to/from Microsoft Azure Blob and File storage, using simple commands designed for optimal performance.
ballgown 2.2.0 ballgown/2.2 None application computational biology Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.
bam-readcount 0.6 bam-readcount/0.6 None application computational biology The purpose of this program is to generate metrics at single nucleotide positions.
bam-readcount 0.8 bam-readcount/0.8 None application computational biology The purpose of this program is to generate metrics at single nucleotide positions.
bamm 1.7.3 bamm/1.7 None application computational biology Metagenomics-focused BAM file manipulation
bamscale 0.0.5 bamscale/0.0.5 None application computational biology BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks
bamtools 2.3.0 bamtools/2.3 None application computational biology C++ API & command-line toolkit for working with BAM data
bamtools 2.4.1 bamtools/2.4 None application computational biology C++ API & command-line toolkit for working with BAM data
bamtools 2.5.1 bamtools/2.5 None application computational biology C++ API & command-line toolkit for working with BAM data
basespace-cli 1.1.0 basespace-cli/1.1 None application biology Toolkit to perform regulatory genomics data analysis
basetools/gapfiller 1.10 basetools/gapfiller/1.10 None application computational biology GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds.
basetools/sspace-standard 3.0 basetools/sspace-standard/3.0 None application computational biology SSPACE-standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data.
bayespeak 1.24.0 bayespeak/1.24.0 None application computational biology This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.
bbmap 37.17 bbmap/37.17 None application computational biology BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bbmap 38.06 bbmap/38.06 None application computational biology BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bbmap 38.84 bbmap/38.84 None application computational biology BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bbmap 39.06 bbmap/39.06 None application computational biology BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bc 1.07.1 bc/1.07 None application Utility bc is an arbitrary precision numeric processing language.
bcftools 1.10.2 bcftools/1.10 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.17 bcftools/1.17 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.2 bcftools/1.2 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.3.1 bcftools/1.3 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.8 bcftools/1.8 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.9 bcftools/1.9 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcl2fastq 1.8.4 bcl2fastq/1.8 None application biology bcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis
bcl2fastq2 2.20.0.422 bcl2fastq2/2.20 None application computational biology The Illumina bcl2fastq2 Conversion Software v2.20 demultiplexes sequencing data and converts base call (BCL) files into FASTQ files.
beagle 4.1_21Jan17.6cc beagle/4.1 None application Biology Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beagle 5.1_24Aug19.3e8 beagle/5.1 None application Biology Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beagle 5.2_21Apr21.304 beagle/5.2 None application Biology Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beagle-lib 4.0.0 beagle-lib/4.0 None application computational biology general purpose library for evaluating the likelihood of sequence evolution on trees
beast 1.10 beast/1.10 None application biology BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast 1.8 beast/1.8 None application biology BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast2 2.4 beast2/2.4 None application biology BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
beast2 2.6.3 beast2/2.6 None application biology BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
beast2 2.7.5 beast2/2.7 None application biology BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
bedops 2.4.35 bedops/2.4 None application computational biology BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
bedtools 2.24.0 bedtools/2.24 None application computational biology A powerful toolset for genome arithmetic
bedtools 2.27.1 bedtools/2.27 None application computational biology A powerful toolset for genome arithmetic
bertopic 0.13.0 bertopic/0.13 None application Modeling BERTopic performs topic Modeling with state-of-the-art transformer models.
beta 1.0.7 beta/1.0 None application computational biology Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
bfc r181 bfc/r181 None application Biology BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data.
bicseq2-norm 0.2.4 bicseq2-norm/0.2 None application bioinformatics BICseq2-norm is for normalizing potential biases in the sequencing data.
bicseq2-seg 0.7.2 bicseq2-seg/0.7 None application bioinformatics BICseq2-seg is for detecting CNVs based on the normalized data given by BICseq2-norm.
bidscoin 4.0.0 bidscoin/py38/4.0 None application neuroimaging Converts and organises raw MRI data-sets according to the Brain Imaging Data Structure (BIDS).
binutils 2.30 binutils/2.30 None application Utilities The GNU Binutils are a collection of binary tools.
binutils 2.35.1 binutils/2.35 None application Utilities The GNU Binutils are a collection of binary tools.
binutils 2.38 binutils/2.38 None application Utilities The GNU Binutils are a collection of binary tools.
bioawk 1.0 bioawk/1.0 None application Biology BWK awk modified for biological data
biobambam 2.0.183 biobambam/2.0 None application computational biology Tools for early stage alignment file processing
bioconductor 3.11 bioconductor/4.0 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.13 bioconductor/r41/3.13 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.14 bioconductor/r41/3.14 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.16 bioconductor/r42/3.16 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.17 bioconductor/r43/3.17 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.18 bioconductor/r43/3.18 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.4 bioconductor/r34/3.6 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.6 bioconductor/3.4 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.8 bioconductor/r35/3.8 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.8 bioconductor/3.8 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 4.0 bioconductor/r40/3.11 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor-ballgown 2.2.0 bioconductor-ballgown/2.2 None application computational biology Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.
bioconductor-jmosaics 1.10 bioconductor-jmosaics/1.10 None application computational biology Joint analysis of multiple ChIP-Seq data sets.
biodata 1.0 biodata/1.0 None application computational biology Static data resources for bioinformatics/computational biology.
biom-format 2.1.10 biom-format/2.1 None application computational biology The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
bioperl 1.6.924 bioperl/1.6 None application computational biology BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
bioperl 1.7.8 bioperl/1.7 None application computational biology BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
biopython 1.70 biopython/py27/1.70 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.70 biopython/py35/1.70 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.70 biopython/py36/1.70 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.71 biopython/py27/1.71 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.71 biopython/py35/1.71 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.71 biopython/py36/1.71 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.74 biopython/py27/1.74 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.74 biopython/py37/1.74 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.76 biopython/py27/1.76 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.76 biopython/py37/1.76 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.77 biopython/py37/1.77 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.77 biopython/py38/1.77 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.79 biopython/py36/1.79 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.79 biopython/py37/1.79 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.79 biopython/py38/1.79 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.79 biopython/py39/1.79 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.81 biopython/py39/1.81 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.81 biopython/py310/1.81 None application biological computation Collection of freely available tools for computational molecular biology
biopython 1.81 biopython/py311/1.81 None application biological computation Collection of freely available tools for computational molecular biology
biosamtools 1.38 biosamtools/1.38 None application computational biology
biser 1.4 biser/1.4 None application computational biology Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies.
bismark 0.14.2 bismark/0.14 None application computational biology Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
bismark 0.19.1 bismark/0.19 None application computational biology Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
bismark 0.24.1 bismark/0.24 None application computational biology Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
bison 3.7.5 bison/3.7 None application Utility General purpose parser generator converting annotated context-free grammar to a deterministic LR/GLR parser.
blast 2.10.0 blast/2.10 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.12.0 blast/2.12 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.13.0 blast/2.13 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.14.0 blast/2.14 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.15.0 blast/2.15 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.2.29 blast/2.2.29 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.2.30 blast/2.2 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.4.0 blast/2.4 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.6.0 blast/2.6 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.7.1 blast/2.7 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast-legacy 2.2.26 blast-legacy/2.2.26 None application computational biology NCBI BLAST sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blat 35 blat/35x1 None application computational biology BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.
blat 35 blat/35 None application computational biology BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.
blat 36 blat/36 None application computational biology BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.
blender 4.2.0 blender/4.2 None application 3D Blender is a free and open-source 3D computer graphics software tool set.
blobtoolkit 4.1.4 blobtoolkit/py39/4.1 None application bioinformatics Interactive quality assessment of genome assemblies.
blobtoolkit 4.1.4 blobtoolkit/py310/4.1 None application bioinformatics Interactive quality assessment of genome assemblies.
blobtools 1.1.1 blobtools/1.1 None application Bioinformatics Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
boa-bacfinder 0.0.2016.02.11 boa-bacfinder/2016.02.11 None application computational biology Find bacteriocins in bacterial genomes
boost 1.44 boost/1.44 None application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.55.0 boost/1.55.0 None application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.66 boost/1.66 compiler/gcc/10 compiler/gcc/9 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.69 boost/1.69 compiler/gcc/9 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.75 boost/1.75 compiler/gcc/9 compiler/intel/18 compiler/intel/20 compiler/gcc/10 compiler/gcc/11 compiler/intel/2021 compiler/intel/19 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boris2 3.0 boris2/3.0 None application Physics Boris Computational Spintronics.
bowtie 1.0 bowtie/1.0 None application computational biology Fast and sensitive read alignment
bowtie 1.1.2 bowtie/1.1 None application computational biology Fast and sensitive read alignment
bowtie 1.3.1 bowtie/1.3 None application computational biology Fast and sensitive read alignment
bowtie 2.2.8 bowtie/2.2 None application computational biology Fast and sensitive read alignment
bowtie 2.3.5 bowtie/2.3 None application computational biology Fast and sensitive read alignment
bowtie 2.4.4 bowtie/2.4 None application computational biology Fast and sensitive read alignment
bowtie 2.5.1 bowtie/2.5 None application computational biology Fast and sensitive read alignment
boxnotes2html 0.1.4 boxnotes2html/0.1 None application Utility Converting from Box Notes to HTML or other formats
bracken 2.6.0 bracken/2.6 None application bioinformatics Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
braker2 2.1.2 braker2/2.1 None application computational biology BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
breakdancer 1.4 breakdancer/1.4 None application computational biology BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
breakseq2 2.2 breakseq2/2.2 None application computational biology BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants.
bsmap 2.90 bsmap/2.90 None application Mapping BSMAP is a short reads mapping software for bisulfite sequencing reads.
busco 3.0.2 busco/py27/3.0 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
busco 3.0.2 busco/py35/3.0 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
busco 3.0.2 busco/py36/3.0 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
busco 4.0.6 busco/py36/4.0 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
busco 5.4.3 busco/py39/5.4 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
bwa 0.6.2 bwa/0.6 None application computational biology Burrow-Wheeler Aligner for short-read alignment.
bwa 0.7.17 bwa/0.7 None application computational biology Burrow-Wheeler Aligner for short-read alignment.
bwa-mem2 2.2.1 bwa-mem2/2.2 None application computational biology The next version of bwa-mem.
bx-python 0.8.1 bx-python/py27/0.8 None application computational biology Tools for manipulating biological data, particularly multiple sequence alignments
bx-python 0.8.1 bx-python/py35/0.8 None application computational biology Tools for manipulating biological data, particularly multiple sequence alignments
bx-python 0.8.1 bx-python/py36/0.8 None application computational biology Tools for manipulating biological data, particularly multiple sequence alignments
bzip2 1.0 bzip2/1.0 compiler/gcc/10 compiler/intel/18 None compiler/gcc/11 compiler/intel/19 compiler/gcc/9 compiler/intel/20 library runtime support
bzip2 1.0.8 bzip2/1.0 compiler/pgi/20 library runtime support
caffe 1.0 caffe/1.0 None application package It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.
caffe-gpu 1.0 caffe-gpu/1.0 None application package It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.
cairo 1.16.0 cairo/1.16 compiler/intel/20 compiler/pgi/20 library runtime support
canu 1.7 canu/1.7 None application computational biology Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
canu 1.8 canu/1.8 None application computational biology Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
canu 2.1.1 canu/2.1 None application computational biology Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
canu 2.2 canu/2.2 None application computational biology Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
cap3 122107 cap3/122107 None application computational biology CAP3: A DNA Sequence Assembly Program
carlsim 3.1 carlsim/3.1 None application computational biology CARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail.
carlsim 4.0 carlsim/4.0 None application computational biology CARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail.
carnac-lr 1.0.0 carnac-lr/1.0 None application computational biology Clustering coefficient-based Acquisition of RNA Communities in Long Read
carveme 1.5.1 carveme/1.5 None application genomics CarveMe is a python-based tool for genome-scale metabolic model reconstruction.
cas-offinder 2.4 cas-offinder/2.4 None application Biology Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
cblaster 1.3.11 cblaster/1.3 None application computational biology Find clustered hits from a BLAST search.
ccat 3.0 ccat/3.0 None application computational biology A software package for the analysis of ChIP-seq data with negative control.
ccp4 7.0 ccp4/7.0 None unknown unknown
cd-hit 4.8.1 cd-hit/4.8 None application Bioinformatics CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cd-hit-auxtools 4.6.8 cd-hit-auxtools/4.6 None application Bioinformatics CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. This module specifically loads the auxillary tools.
cdna-cupcake-tofu2 5.2 cdna-cupcake-tofu2/5.2 None application computational biology cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
cdo 1.9.7.1 cdo/1.9 None application Utilities CLI tools to manipulate and analyse Climate and NWP model Data
cdo 2.4.0 cdo/2.4 None application Utilities CLI tools to manipulate and analyse Climate and NWP model Data
cdsapi 0.6.1 cdsapi/py39/0.6 None application Copernicus Climate Data Store API to access the Copernicus Climate Data Store at ECMWF
cdsapi 0.6.1 cdsapi/py310/0.6 None application Copernicus Climate Data Store API to access the Copernicus Climate Data Store at ECMWF
cdsapi 0.6.1 cdsapi/py311/0.6 None application Copernicus Climate Data Store API to access the Copernicus Climate Data Store at ECMWF
cdsapi 0.7.2 cdsapi/py310/0.7 None application Copernicus Climate Data Store API to access the Copernicus Climate Data Store at ECMWF
cdsapi 0.7.2 cdsapi/py312/0.7 None application Copernicus Climate Data Store API to access the Copernicus Climate Data Store at ECMWF
cellranger 3.0.2 cellranger/3.0 None application computational biology Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
cenote-taker2 2.1.2 cenote-taker2/2.1 None application computational biology Cenote-Taker2 is a pipeline for divergent virus discovery and annotation.
cenote-taker2 2020.04.01 cenote-taker2/2020.04.01 None application computational biology Cenote-Taker2 is a pipeline for divergent virus discovery and annotation.
cexor 1.10 cexor/1.10 None application computational biology An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates.
cgmaptools 0.1.2 cgmaptools/0.1 None application computational biology Command-line Toolset for Bisulfite Sequencing Data Analysis
checkm-genome 1.0.18 checkm-genome/1.0 None application computational biology Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
checkm-genome 1.1.2 checkm-genome/1.1 None application computational biology Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
checkm2 1.0.1 checkm2/1.0 None application bioinformatics CheckM2 - Predicting the quality of metagenome-recovered bins
checkv 0.7.0 checkv/0.7 None application Biology Assess the quality of metagenome-assembled viral genomes.
checkv 0.8.1 checkv/0.8 None application Biology Assess the quality of metagenome-assembled viral genomes.
chemdata 1.0 chemdata/1.0 None application computational chemistry Static data resources for computational chemistry (docking, etc.).
chewbbaca 2.8.4 chewbbaca/2.8 None application computational biology A complete suite for gene-by-gene schema creation and strain identification.
chromosomer 0.1.4a chromosomer/0.1.4a None application Bioinformatics A reference-assisted assembly tool for producing draft chromosome sequences.
circlator 1.5.5 circlator/1.5 None application Biology circlator: a tool to circularise genome assemblies
circleator 1.0.2 circleator/1.0 None application computational biology Flexible circular visualization of genome-associated data with BioPerl and SVG.
cite-seq-count 1.4.4 cite-seq-count/1.4 None application Bioinformatics A python package to map reads from CITE-seq or hashing data for single cell experiments
clark 1.2 clark/1.2 None application computational biology
clearcut 1.0 clearcut/1.0 None application computational biology Clearcut - The reference implementation for Relaxed Neighbor Joining (RNJ)
clove 0.17 clove/0.17 None application computational biology CLOVE: Classification of genomic fusions into structural variation events.
clustal-omega 1.2 clustal-omega/1.2 None application computational biology Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours
clustalw 2.1 clustalw/2.1 None application computational biology ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences.
cmake 2.8.10.2 cmake/2.8 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.10.3 cmake/3.10 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.11.3 cmake/3.11 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.14.5 cmake/3.14 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.17.0 cmake/3.17 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.20.5 cmake/3.20 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.28.3 cmake/3.28 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.5.0 cmake/3.5 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.7.1 cmake/3.7 None application system CMake is an extensible, open-source system that manages the build process
cnvcaller 0.0.2024.01.18 cnvcaller/2024.01.18 None application computational biology CNVcaller is designed to detect copy number variation using sequencing data from populations.
cnvkit 0.9.10 cnvkit/0.9 None application bioinformatics Copy number variant detection from high-throughput sequencing
cobra 0.17.1 cobra/py36/0.17 None application Biology COBRApy is a package for constraints-based modeling of metabolic networks.
cobra 0.17.1 cobra/py37/0.17 None application Biology COBRApy is a package for constraints-based modeling of metabolic networks.
cobra 0.26.3 cobra/py38/0.26 None application Biology COBRApy is a package for constraints-based modeling of metabolic networks.
cobra 0.26.3 cobra/py39/0.26 None application Biology COBRApy is a package for constraints-based modeling of metabolic networks.
cobra 0.26.3 cobra/py310/0.26 None application Biology COBRApy is a package for constraints-based modeling of metabolic networks.
code-server 4.17.1 code-server/4.17 None application Development VS Code in the browser.
code-server 4.89.1 code-server/4.89 None application Development VS Code in the browser.
codonw 1.4.4 codonw/1.4 None application computational biology CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage.
cogent 3.1 cogent/3.1 None application computational biology Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.
coin-or 1.8 coin-or/1.8 compiler/gcc/9 library Open-source mixed integer linear programming solver
colony2 20230425 colony2/20230425 compiler/intel/18 compiler/gcc/9 application computational biology
compass-cplex 0.2022.04.02 compass-cplex/2022.04.02 None application bioinformatics In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes.
compiler/clang 13 compiler/clang/13 None application compiler
compiler/clang 17 compiler/clang/17 None application compiler
compiler/clang 18 compiler/clang/18 None application compiler
compiler/gcc 10 compiler/gcc/10 None application compiler
compiler/gcc 11 compiler/gcc/11 None application compiler
compiler/gcc 12 compiler/gcc/12 None application compiler
compiler/gcc 13.2 compiler/gcc/13 None application compiler
compiler/gcc 14.2 compiler/gcc/14 None application compiler
compiler/gcc 9 compiler/gcc/9 None application compiler
compiler/intel 18 compiler/intel/18 None application compiler
compiler/intel 19 compiler/intel/19 None application compiler
compiler/intel 20 compiler/intel/20 None application compiler
compiler/intel 2021.5 compiler/intel/2021 None application compiler
compiler/intel 2024.2 compiler/intel/2024 None application compiler
compiler/nvhpc 21.9 compiler/nvhpc/21.9 None application compiler NVIDIA HPC SDK for Linux.
compiler/nvhpc 24.5 compiler/nvhpc/24.5 None application compiler NVIDIA HPC SDK for Linux.
compiler/pgi 18 compiler/pgi/18 None application compiler
compiler/pgi 19 compiler/pgi/19 None application compiler
compiler/pgi 20 compiler/pgi/20 None application compiler
compleasm 0.2.6 compleasm/0.2 None application bioinformatics Compleasm: a faster and more accurate reimplementation of BUSCO
comsol 5.4 comsol/5.4 None application simulation COMSOL Multiphysics
comsol 5.5 comsol/5.5 None application simulation COMSOL Multiphysics
comsol 5.6 comsol/5.6 None application simulation COMSOL Multiphysics
comsol 6.0 comsol/6.0 None application simulation COMSOL Multiphysics
concoct 1.1.0 concoct/1.1 None application Genomics Clustering cONtigs with COverage and ComposiTion
conn 18b conn/18b None application matlab toolbox CONN is a Matlab-based cross-platform software for the computation, display, and analysis of functional connectivity in fMRI (fcMRI).
connectome-workbench 1.3.2 connectome-workbench/1.3 None application neuroimaging Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project
consurf 1.0.0 consurf/1.0 None application Biology Stand Alone version of ConSurf
conterminator 1.c74b5 conterminator/1.c74b5 None application computational biology Efficient method for detecting incorrectly labeled sequences across kingdoms
convert3d 1.3.0 convert3d/1.3 None application utility ITK-based image manipulation tool
coreutils 8.31 coreutils/8.31 None application shell tool The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system.
corretto-jdk 11 corretto-jdk/11 None application system Amazon Corretto (Java).
corretto-jdk 17 corretto-jdk/17 None application system Amazon Corretto (Java).
corretto-jdk 21 corretto-jdk/21 None application system Amazon Corretto (Java).
corretto-jdk 22 corretto-jdk/22 None application system Amazon Corretto (Java).
corretto-jdk 8 corretto-jdk/8 None application system Amazon Corretto (Java).
cosmomvpa d43b0e7 cosmomvpa/d43b0e7 None application matlab toolbox A multi-modal, multi-variate pattern analysis (MVPA) toolbox in Matlab and GNU Octave for cognitive neuroscientists.
coverm 0.6.1 coverm/0.6 None application computational biology CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications
cp2k 2023.1 cp2k/2023.1 compiler/intel/20:openmpi/4.1 compiler/gcc/10:openmpi/4.1 application quantum chemistry Quantum chemistry and solid state physics software package
cp2k 2024.3 cp2k/2024.3 compiler/intel/20:openmpi/4.1 application quantum chemistry Quantum chemistry and solid state physics software package
cp2k 8.2.0 cp2k/8.2 compiler/gcc/10:openmpi/4.1 application quantum chemistry Quantum chemistry and solid state physics software package
cp2k 9.1 cp2k/9.1 compiler/intel/20:openmpi/4.1 application quantum chemistry Quantum chemistry and solid state physics software package
cp2k 9.1.0 cp2k/9.1 compiler/gcc/10:openmpi/4.1 application quantum chemistry Quantum chemistry and solid state physics software package
crest 1.0 crest/1.0 None application computational biology
crossmap 0.7.0 crossmap/0.7 None application bioinformatics CrossMap is a program for convenient conversion of genome coordinates and genome annotation files between assemblies.
csaw 1.4 csaw/1.4 None application computational biology Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
cuda 10.0 cuda/10.0 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 10.2 cuda/10.2 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 11.0 cuda/11.0 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 11.2 cuda/11.2 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 11.4 cuda/11.4 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 11.6 cuda/11.6 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 11.8 cuda/11.8 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 12.2 cuda/12.2 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 6.0 cuda/6.0 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 6.5 cuda/6.5 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 7.5 cuda/7.5 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 8.0 cuda/8.0 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 9.0 cuda/9.0 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 9.1 cuda/9.1 None application compiler NVIDIA CUDA Toolkit for Linux.
cuda 9.2 cuda/9.2 None application compiler NVIDIA CUDA Toolkit for Linux.
cudnn v5 cudnn/v5 None application compiler NVIDIA cuDNN Toolkit for Linux.
cufflinks 2.1 cufflinks/2.1 None application computational biology Transcriptome assembly and differential expression analysis for RNA-Seq.
cufflinks 2.2.1 cufflinks/2.2 None application computational biology Transcriptome assembly and differential expression analysis for RNA-Seq.
curl 7.50 curl/7.50 None application network
curl 7.76 curl/7.76 compiler/gcc/11 compiler/intel/19 compiler/gcc/10 compiler/intel/20 compiler/gcc/9 compiler/intel/2021 application network
cutadapt 1.13 cutadapt/1.13 None application NGS data Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt 1.4 cutadapt/1.4 None application NGS data Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt 2.8 cutadapt/2.8 None application NGS data Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt 2.9 cutadapt/2.9 None application NGS data Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutruntools 2020.07.10 cutruntools/2020.07.10 None application computational biology CUT&RUNTools is a flexible pipeline for CUT&RUN processing and footprint analysis.
cytoscape 3.10.1 cytoscape/3.10 None unknown unknown Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
cytoscape 3.6 cytoscape/3.6 None unknown unknown Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
das_tool 1.1.2 das_tool/1.1 None application Genomics Recovery of genomes from metagenomes via a dereplication,aggregation and scoring strategy.
dastk 1.0.0 dastk/1.0 None application Bioinformatics Differential ATAC-seq toolkit
dcm2niix 1.0.20230411 dcm2niix/1.0 None application neuroimaging dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.
deap 1.0 deap/1.0 None application computer science DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas.
dedalus 2.1905 dedalus/py37/2.1905 None application partial differential equation A flexible framework for solving differential equations using spectral methods.
dedalus 2.2006 dedalus/py37/2.2006 None application partial differential equation A flexible framework for solving differential equations using spectral methods.
dedalus 2.2207.3 dedalus/2.2207 compiler/gcc/11:openmpi/4.1 application partial differential equation A flexible framework for solving differential equations using spectral methods.
dedup 0.12.8 dedup/0.12 None application DNA sequencing DeDup is a tool for read deduplication in paired-end read merging
deepmd-kit 2.0.3 deepmd-kit/2.0 None application molecular dynamics Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit 2.2.5 deepmd-kit/py39/2.2 None application molecular dynamics Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit 2.2.5 deepmd-kit/py310/2.2 None application molecular dynamics Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit-gpu 2.0.3 deepmd-kit-gpu/2.0 None application molecular dynamics Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit-gpu 2.2.5 deepmd-kit-gpu/py39/2.2 None application molecular dynamics Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit-gpu 2.2.5 deepmd-kit-gpu/py310/2.2 None application molecular dynamics Deep learning package for many-body potential energy representation and molecular dynamics.
deeptools 2.5.4 deeptools/2.5 None application computational biology
deeptools 3.0.2 deeptools/3.0 None application computational biology
deeptools 3.5.1 deeptools/3.5 None application computational biology
deepvirfinder 2020.11.21 deepvirfinder/2020.11.21 None application metagenomics Identifying viruses from metagenomic data by deep learning.
defiant 2019.03.02 defiant/2019.03.02 None application computational biology Differential methylation, Easy, Fast, Identification and ANnoTation.
delly 0.8.3 delly/0.8 None application Biology Structural variant discovery by integrated paired-end and split-read analysis
delly 0.9.1 delly/0.9 None application Biology Structural variant discovery by integrated paired-end and split-read analysis
delly-omp 0.8.3 delly-omp/0.8 None application Biology Structural variant discovery by integrated paired-end and split-read analysis.
demultiplex 1.2.2 demultiplex/1.2 None application Genomics Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes
desman 2.1 desman/2.1 None application computational biology De novo Extraction of Strains from MetAgeNomes
detectron 2018.09.11 detectron/py27/2018.09.11 None application object detection FAIR's research platform for object detection research, implementing popular algorithms like Mask R-CNN and RetinaNet.
detectron2 0.2.1 detectron2/py37/0.2 None application object detection Detectron2 is FAIR's next-generation platform for object detection and segmentation.
dftd4 3.3.0 dftd4/3.3 compiler/intel/19 compiler/gcc/10 compiler/gcc/9 compiler/intel/20 application Physics
diamond 0.9.25 diamond/0.9 None application Computational Biology Accelerated BLAST compatible local sequence aligner
diamond 2.0.9 diamond/2.0 None application Computational Biology Accelerated BLAST compatible local sequence aligner
diamond 2.1.9 diamond/2.1 None application Computational Biology Accelerated BLAST compatible local sequence aligner
diffsplice 0.1.11 diffsplice/0.1 None application computational biology DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq
dmtcp 2.0 dmtcp/2.0 None application Utility
dmtcp 2.3 dmtcp/2.3 None application Utility
dmtcp 2.4 dmtcp/2.4 None application Utility
dmtcp 2.5 dmtcp/2.5 None application Utility
dmtcp 2.6 dmtcp/2.6 compiler/gcc/10 None compiler/intel/19 compiler/gcc/9 compiler/intel/20 application Utility
dorado 0.4.2 dorado/0.4 None application bioinformatics Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado 0.6.0 dorado/0.6 None application bioinformatics Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado 0.7.2 dorado/0.7 None application bioinformatics Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado-gpu 0.4.2 dorado-gpu/0.4 None application bioinformatics Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado-gpu 0.6.0 dorado-gpu/0.6 None application bioinformatics Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado-gpu 0.7.2 dorado-gpu/0.7 None application bioinformatics Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dram 1.0.6 dram/1.0 None application genomics Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
dram 1.2.0 dram/1.2 None application genomics Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
dram 1.5.0 dram/1.5 None application genomics Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
drep 2.3.2 drep/2.3 None application Biology De-replication of microbial genomes assembled from multiple samples
dsk 2.3.3 dsk/2.3 None application computational biology DSK is a k-mer counter for reads or genomes.
dssp 4.4.7 dssp/4.4 None application computational biology Application to assign secondary structure to proteins.
dtiprep 1.2 dtiprep/1.2 None application unknown DTIPrep is a neuroimaging tool that performs a Study-specific Protocol based automatic pipeline for DWI/DTI quality control and preparation.
ea-utils 1.01 ea-utils/1.0 None application computational biology EA Utils is a collection of command line tools for processing NextGen sequencing data. Included are fastq-stats and sam-stats which are lightweight tools that display a variety of statistics on fastq and sam files.
eccodes 2.24.2 eccodes/2.24 compiler/intel/20 compiler/gcc/10 compiler/pgi/20 compiler/intel/19 compiler/gcc/9 application package
effector-p 2.0 effector-p/2.0 None application Biology EffectorP is a machine learning method for fungal effector prediction in secretomes.
eggnog-mapper 2.1.3 eggnog-mapper/2.1 None application Biology Fast genome-wide functional annotation through orthology assignment.
eigen 3.3.3 eigen/3.3 None application C++ C++ template library for linear algebra
eigen 3.4.0 eigen/3.4 None application C++ C++ template library for linear algebra
eigensoft 8.0.0 eigensoft/8.0 None application genomics The EIGENSOFT package implements methods for analzing population structure and performing stratification correction
elk 8.7.10 elk/8.7 compiler/intel/20:openmpi/4.0 library runtime support
elk 9.5.1 elk/9.5 compiler/intel/20:openmpi/4.0 library runtime support
emacs 26.2 emacs/26.2 None application Utility GNU Emacs is an extensible, customizable text editor.
emacs 27.2 emacs/27.2 None application Utility GNU Emacs is an extensible, customizable text editor.
emacs 28.2 emacs/28.2 None application Utility GNU Emacs is an extensible, customizable text editor.
emacs 29.3 emacs/29.3 None application Utility GNU Emacs is an extensible, customizable text editor.
eman2 2022.11.06 eman2/2022.11.06 compiler/gcc/10:openmpi/4.1 compiler/gcc/9:openmpi/4.1 application image processing A scientific image processing software suite with a focus on CryoEM and CryoET.
emboss 6.5.7 emboss/6.5 None application computational biology EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
emboss 6.6.0 emboss/6.6 None application computational biology EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
emirge 0.61.1 emirge/0.61 None application Biology EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
ensembl-vep 104.3 ensembl-vep/104.3 None application Biology The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
ensembl-vep 96.0 ensembl-vep/96.0 None application Biology The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
ensembl-vep 99.2 ensembl-vep/99.2 None application Biology The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
entrez-direct 10.0 entrez-direct/10.0 None application Entrez Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
entrez-direct 11.0 entrez-direct/11.0 None application Entrez Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
entrez-direct 13.3 entrez-direct/13.3 None application Entrez Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
entrez-direct 16.2 entrez-direct/16.2 None application Entrez Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
epic2 0.0.50 epic2/0.0.50 None application Biology Ultraperformant Chip-Seq broad domain finder based on SICER.
epivia 1.1.2 epivia/1.1 None application Epigenomics Virial Integration Analysis with epigenetic data
epoch 4.17.16 epoch/4.17 compiler/intel/20:openmpi/4.0 application Applications
epoch 4.17.16 epoch/4.19 compiler/intel/20:openmpi/4.0 application Applications
eqtlbma 1.3 eqtlbma/1.3 None application biology Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.
erne 2.1.1 erne/2.1 None application computational biology ERNE is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
esmf 8.2.0 esmf/8.2 compiler/intel/19:openmpi/4.0 application Utility
espresso 6.8 espresso/6.8 compiler/intel/20:openmpi/4.0 compiler/intel/20:openmpi/4.1 library runtime support
espresso 7.0 espresso/7.0 compiler/intel/20:openmpi/4.1 library runtime support
espresso 7.1 espresso/7.1 compiler/intel/20:openmpi/4.1 compiler/intel/20:openmpi/4.0 library runtime support
espresso 7.3 espresso/7.3 compiler/intel/20:openmpi/4.1 compiler/intel/20:openmpi/4.0 library runtime support
espresso-gpu 7.1 espresso-gpu/7.1 compiler/nvhpc/21.9:openmpi/3.1 library runtime support
espresso-gpu 7.3 espresso-gpu/7.3 compiler/nvhpc/21.9:openmpi/3.1 library runtime support
espresso-plumed 6.2 espresso-plumed/6.2 compiler/intel/20:openmpi/4.1 library runtime support
ete3 3.1.1 ete3/3.1 None application NCBI Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
evidencemodeler 1.1.1 evidencemodeler/1.1 None application computational biology EVidence Modeler.
exomiser 7.2 exomiser/7.2 None application computational biology The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data.
exonerate 2.2.0 exonerate/2.2 None application computational biology Exonerate - A generic tool for pairwise sequence comparison / alignment
exonerate 2.4.0 exonerate/2.4 None application computational biology Exonerate - A generic tool for pairwise sequence comparison / alignment
expansionhunterdenovo 0.9.0 expansionhunterdenovo/0.9 None application computational biology ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
expat 2.2.9 expat/2.2 compiler/pgi/20 compiler/intel/20 compiler/gcc/9 compiler/intel/19 compiler/gcc/10 library runtime support
export2graphlan 0.20 export2graphlan/0.20 None application bioinformatics export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn.
express 1.5 express/1.5 None application life sciences express - Streaming quantification for high-throughput sequencing
fair-esm 2.0.0 fair-esm/py39/2.0 None application evolutionary modeling Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fair-esm 2.0.0 fair-esm/py310/2.0 None application evolutionary modeling Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fair-esm-gpu 2.0.0 fair-esm-gpu/py39/2.0 None application evolutionary modeling Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fair-esm-gpu 2.0.0 fair-esm-gpu/py310/2.0 None application evolutionary modeling Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fargene 0.1 fargene/0.1 None application bioinformatics Fragmented Antibiotic Resistance Gene iENntifiEr takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output
fastani 1.32 fastani/1.32 None application Biology FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
fastcluster 1.2.6 fastcluster/py39/1.2 None application machine learning Fast hierarchical clustering routines for R and Python.
fastcluster 1.2.6 fastcluster/py310/1.2 None application machine learning Fast hierarchical clustering routines for R and Python.
fastp 0.23.2 fastp/0.23 None application bioinformatics A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...)
fastq-screen 0.15.3 fastq-screen/0.15 None application computational biology FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect
fastq_utils 0.25.2 fastq_utils/0.25 None application Genomics Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
fastqc 0.10.1 fastqc/0.10 None application computational biology fastqc - A Quality Control application for FastQ files
fastqc 0.11.7 fastqc/0.11 None application computational biology fastqc - A Quality Control application for FastQ files
fastqc 0.12.1 fastqc/0.12 None application computational biology fastqc - A Quality Control application for FastQ files
fastspar 0.0.10 fastspar/0.0.10 None application computational biology Rapid and scalable correlation estimation for compositional data
faststructure 1.0 faststructure/1.0 None application computational biology A variational framework for inferring population structure from SNP genotype data.
fasttree 2.1.11 fasttree/2.1 None application computational biology FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
fastx_toolkit 0.0.14 fastx_toolkit/0.0.14 None application computational biology FASTX Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
fegenie 1.0 fegenie/1.0 None application genomics HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes.
feh 3.3 feh/3.3 None application Utility feh is an X11 image viewer aimed mostly at console users.
feh 3.9.1 feh/3.9 None application Utility feh is an X11 image viewer aimed mostly at console users.
fenics 2018.1.0 fenics/2018.1 None application partial differential equations FEniCS is a collection of free software for automated, efficient solution of differential equations
ffmpeg 4.3.1 ffmpeg/4.3 None application Utility Cross-platform solution to record, convert and stream audio and video.
ffmpeg 4.4.1 ffmpeg/4.4 None application Utility Cross-platform solution to record, convert and stream audio and video.
fftw3 3.3 fftw3/3.3 compiler/gcc/10 compiler/gcc/9:openmpi/4.0 compiler/intel/19:openmpi/4.1 compiler/gcc/11 compiler/intel/20:openmpi/4.0 compiler/intel/18:openmpi/4.0 compiler/gcc/10:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/gcc/10:openmpi/4.1 compiler/intel/18:openmpi/4.1 compiler/intel/19 compiler/pgi/20 compiler/gcc/11:openmpi/4.0 compiler/pgi/20:openmpi/4.1 compiler/gcc/9:openmpi/4.1 compiler/intel/18 compiler/intel/20:openmpi/4.1 compiler/intel/20 compiler/gcc/9 None compiler/pgi/20:openmpi/4.0 compiler/gcc/11:openmpi/4.1 library runtime support
fgbio 0.8.0 fgbio/0.8 None application Genomics A set of tools for working with genomic and high throughput sequencing data, including UMIs
figtree 1.4.4 figtree/1.4 None application Utilities FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.
fiji 20220414 fiji/20220414 None application Image Processing Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
flash 1.2.11 flash/1.2 None application bioinformatics Merge paired sequencing reads into single longer sequences
flash2 2.2.00 flash2/2.2 None application bioinformatics Merge paired-end reads from fragments that are shorter than twice the read length
fleur 6.2 fleur/6.2 compiler/gcc/11:openmpi/4.1 application physics A feature-full, freely available FLAPW (full-potential linearized augmented planewave) code, based on density-functional theory.
fleur 7.0 fleur/7.0 compiler/gcc/9:openmpi/4.1 application physics A feature-full, freely available FLAPW (full-potential linearized augmented planewave) code, based on density-functional theory.
flex 3.7.5 flex/2.6 None application Utility General purpose parser generator converting annotated context-free grammar to a deterministic LR/GLR parser.
flye 2.8.3 flye/2.8 None application Bioinformatics Fast and accurate de novo assembler for single molecule sequencing reads
flye 2.9.1 flye/2.9 None application Bioinformatics Fast and accurate de novo assembler for single molecule sequencing reads
foldseek 8.ef4e960 foldseek/8.ef4e960 None application computational bioinformatics Foldseek: fast and accurate protein structure search
foldseek 9.427df8a foldseek/9.427df8a None application computational bioinformatics Foldseek: fast and accurate protein structure search
fonduer 0.8.2 fonduer/py37/0.8 None application knowledge base Fonduer is a Python package and framework for building knowledge base construction (KBC) applications from richly formatted data.
fortrangis 2.5 fortrangis/2.5 compiler/gcc/10 compiler/intel/20 compiler/gcc/9 compiler/intel/19 library runtime support
fqtrim 0.9.7 fqtrim/0.9 None application computational biology fqtrim: trimming & filtering of NGS reads.
fragpipe 20.0 fragpipe/20.0 None application mass spectrometry Pipeline for comprehensive analysis of shotgun proteomics data
freebayes 1.2.0 freebayes/1.2 None application Biology Bayesian haplotype-based polymorphism discovery and genotyping
freebayes 1.3.7 freebayes/1.3 None application Biology Bayesian haplotype-based polymorphism discovery and genotyping
freecad 0.20.1 freecad/0.20 None application 3D modeling FreeCAD is a parametric 3D modeler made primarily to design real-life objects of any size.
freesurfer 5.3.0 freesurfer/5.3 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer 6.0.1 freesurfer/6.0 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer 7.1.1 freesurfer/7.1 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer 7.2.0 freesurfer/7.2 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer 7.4.1 freesurfer/7.4 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
freetype 2.10.0 freetype/2.10 compiler/intel/20 compiler/pgi/20 library runtime support
fsl 6.0.6 fsl/6.0 None application computational neuroimaging FMRIB Software Library
fusioncatcher 1.33 fusioncatcher/1.33 None application computational biology Finder of Somatic Fusion Genes in RNA-seq data.
gamess 20210930R2 gamess/20210930R2 compiler/intel/2021:intel-mpi/2021 compiler/intel/19:openmpi/4.0 library runtime support
gamess-omp 20210930R2 gamess-omp/20210930R2 compiler/intel/19:openmpi/4.0 library runtime support
gap 4.11.0 gap/4.11 None application Mathematics GAP - Groups, Algorithms, Programming, a System for Computational Discrete Algebra
gapfiller 2.1.1 gapfiller/2.1 None application computational biology GapFiller is a seed-and-extend local assembler to fill the gap within paired reads.
gat 1.3.6 gat/1.3 None application Biology Genomic Association Tester
gatk 3.4-46 gatk/3.4 None application computational biology The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gatk 3.7 gatk/3.7 None application computational biology The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gatk4 4.0.4.0 gatk4/4.0 None application computational biology GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4 4.1.8.1 gatk4/4.1 None application computational biology GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4 4.2.4.1 gatk4/4.2 None application computational biology GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4 4.3.0.0 gatk4/4.3 None application computational biology GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4 4.4.0.0 gatk4/4.4 None application computational biology GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gaussian 09 RevD gaussian/09/RevD None application Chemistry
gaussian 09 RevE gaussian/09/RevE None application Chemistry
gaussian 16 RevA gaussian/16/RevA None application Chemistry
gbmunge 2018.07.06 gbmunge/2018.07.06 None application computational biology Munge GenBank files into FASTA and tab-separated metadata.
gcprofile 1.0 gcprofile/1.0 None application computational biology GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
gcta 1.94.1 gcta/1.94 None application computational biology GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits.
gdal 3.4 gdal/3.4 compiler/gcc/10 compiler/gcc/9 compiler/intel/20 compiler/intel/19 library runtime support
gdcclient 1.3.0 gdcclient/1.3 None application genomics GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gdcclient 1.4.0 gdcclient/1.4 None application genomics GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gdcclient 1.6.1 gdcclient/1.6 None application genomics GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gem 2.7 gem/2.7 None application computational biology GEM: High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data.
gemma 0.98.1 gemma/0.98 None application computational biology Linear mixed models (LMMs) for genome-wide association (GWA)
gemoma 1.9 gemoma/1.9 None application Genome Analysis Gene Model Mapper (GeMoMa) is a homology-based gene prediction program.
genemark-es 2.3f genemark-es/2.3f None application computational biology GeneMark-ES.
genemarks 2.5p genemarks/2.5p None application computational biology GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
genemarks 4.3 genemarks/4.3 None application computational biology GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
genodiver 2018.11.12 genodiver/2018.11.12 None application biology Geno-Diver is a complex animal genetic simulation tool that is able to simulate quantitative and/or fitness characters.
genometester4 4.0 genometester4/4.0 None application Bioinformatics A toolkit for performing set operations - union, intersection and complement - on k-mer lists.
genometools/py27 1.5.10 genometools/py27/1.5 None application Bioinformatics GenomeTools genome analysis system.
genometools/py35 1.5.10 genometools/py35/1.5 None application Bioinformatics GenomeTools genome analysis system.
genometools/py36 1.5.10 genometools/py36/1.5 None application Bioinformatics GenomeTools genome analysis system.
genozip 14.0.21 genozip/14.0 None application computational biology Compressor for genomic files (FASTQ, BAM, VCF, FASTA and more), up to 5x better than gzip and faster too
gensim 3.8.0 gensim/py27/3.8 None application Machine learning Topic Modelling for Humans
gensim 3.8.0 gensim/py36/3.8 None application Machine learning Topic Modelling for Humans
gensim 3.8.0 gensim/py37/3.8 None application Machine learning Topic Modelling for Humans
geodata 1.0 geodata/1.0 None application geo models Static data resources for geo data.
geoparse 1.0.5 geoparse/1.0 None application Bioinformatics Python library to access Gene Expression Omnibus Database (GEO)
geos 3.8 geos/3.8 compiler/gcc/10 compiler/pgi/20 compiler/gcc/9 compiler/intel/20 compiler/intel/19 library runtime support
getorganelle 1.7.7.1 getorganelle/1.7 None application bioinformatics Get organelle genomes from genome skimming data
gffcompare 0.10.6 gffcompare/0.10 None application Annotation GffCompare by Geo Pertea
gffread 0.12.7 gffread/0.12 None application bioinformatics GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.
gflags 2.1 gflags/2.1 None library unknown Online documentation available at: https://gflags.github.io/gflags/
ghostscript 9.20 ghostscript/9.20 None library runtime support An interpreter for the PostScript language and for PDF.
ghostscript 9.22 ghostscript/9.22 None library runtime support An interpreter for the PostScript language and for PDF.
gistic2 2.0.23 gistic2/2.0 None application Biology GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
git 2.17.0 git/2.17 None library tools distributed version control system
git 2.22.0 git/2.22 None library tools distributed version control system
git 2.29.2 git/2.29 None library tools distributed version control system
git 2.30.9 git/2.30 None library tools distributed version control system
git 2.35.8 git/2.35 None library tools distributed version control system
git 2.39.3 git/2.39 None library tools distributed version control system
git 2.40.1 git/2.40 None library tools distributed version control system
git 2.7.4 git/2.7 None library tools distributed version control system
globalarrays 5.8.2 globalarrays/5.8 compiler/gcc/11:openmpi/4.1 compiler/gcc/9:openmpi/4.1 compiler/intel/20:openmpi/4.1 compiler/intel/19:openmpi/4.1 compiler/intel/2021:openmpi/4.1 compiler/gcc/10:openmpi/4.1 library runtime support
globus-cli 1.10.1 globus-cli/1.10 None application tool Globus CLI
globus-cli 1.13.0 globus-cli/1.13 None application tool Globus CLI
globus-cli 1.2.0 globus-cli/1.2 None application tool Globus CLI
globus-cli 2.0.0 globus-cli/2.0 None application tool Globus CLI
globus-cli 3.18.0 globus-cli/3.0 None application tool Globus CLI
glog 0.3.3 glog/0.3 None application Utility
glpk 4.61 glpk/4.61 None application mathematics The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
gmap 2015.12.31 gmap/2015.12.31 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap 2017.05.08 gmap/2017.05.08 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap 2018.03.25 gmap/2018.03.25 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap 2020.04.08 gmap/2020.04.08 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap 2021.08.25 gmap/2021.08.25 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap 2023.10.10 gmap/2023.10.10 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmcloser 1.6.2 gmcloser/1.6 None application computational biology GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.
gmp 6.2.1 gmp/6.2 compiler/pgi/20 compiler/gcc/9 compiler/intel/20 compiler/intel/19 compiler/gcc/10 library runtime support GNU MP is a library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
gmx_mmpbsa 1.6.3 gmx_mmpbsa/1.6 compiler/gcc/11:openmpi/4.1 application computational chemistry gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
gnu-parallel 20180522 gnu-parallel/20180522 None application Shell tool GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
gnu-parallel 20220722 gnu-parallel/20220722 None application Shell tool GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
gnuplot 4.6.0 gnuplot/4.6 None application unknown Gnuplot, plotting from command line
gnuplot 5.2.3 gnuplot/5.2 None application unknown Gnuplot, plotting from command line
gnuplot 5.4.1 gnuplot/5.4 None application unknown Gnuplot, plotting from command line
google-cloud-sdk 350.0.0 google-cloud-sdk/350 None application Utility Command-line interface for Google Cloud Platform products and services
google-cloud-sdk 440.0.0 google-cloud-sdk/440 None application Utility Command-line interface for Google Cloud Platform products and services
gradle 3.3 gradle/3.3 None application Utility Gradle - an open-source build-automation system
gradle 5.6 gradle/5.6 None application Utility Gradle - an open-source build-automation system
gradle 7.1.0 gradle/7.1 None application Utility Gradle - an open-source build-automation system
gramalign 3.0 gramalign/3.0 None application computational biology GramAlign is a time-efficient progressive Multiple Sequence Alignment (MSA) algorithm.
gramcluster 1.3 gramcluster/1.3 None application computational biology GramCluster is a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.
gramdist 1.0 gramdist/1.0 None application computational biology GramDist is a utility for generating dissimilarity matrices using the relative complexity measure, a computationally efficient and alignment free evolutionary distance metric.
graphlan 1.0.0 graphlan/1.0 None application computational biology GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
graphlan 1.1.2 graphlan/1.1 None application computational biology GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
graphviz 2.38.0 graphviz/2.38 None application Visualization Open Source graph visualization software.
graphviz 2.40.1 graphviz/2.40 None application Visualization Open Source graph visualization software.
graphviz 4.0.0 graphviz/4.0 None application Visualization Open Source graph visualization software.
grib-api 1.21.0 grib-api/1.21 compiler/pgi/20 compiler/intel/20 library runtime support
gromacs 2022.3 gromacs/2022.3 compiler/gcc/10:openmpi/4.1 application computational biology GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs 2023 gromacs/2023 compiler/gcc/10:openmpi/4.1 application computational biology GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs 2024.1 gromacs/2024.1 compiler/gcc/11:openmpi/4.1 application computational biology GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu 2021.1 gromacs-gpu/2021.1 compiler/gcc/9 application computational biology GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu 2022.3 gromacs-gpu/2022.3 compiler/gcc/10 application computational biology GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu 2023 gromacs-gpu/2023 compiler/gcc/10 compiler/gcc/10:openmpi/4.1 application computational biology GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu 2024.1 gromacs-gpu/2024.1 compiler/gcc/11 compiler/gcc/11:openmpi/4.1 application computational biology GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
groopm 0.3.4 groopm/0.3 None application bioinformatics Metagenomic binning suite
gstreamer 1.20.3 gstreamer/1.20 None application Library for constructing graphs of media-handling components Library for constructing graphs of media-handling components
gstreamer 1.22.5 gstreamer/1.22 None application Library for constructing graphs of media-handling components Library for constructing graphs of media-handling components
gsufsort 2023.10.20 gsufsort/2023.10.20 None application bioinformatics Building suffix arrays, LCP-arrays and BWTs for string collections.
gsutil 350.0.0 gsutil/4.65 None application Utility Command-line interface for Google Cloud Platform products and services
gsutil 440.0.0 gsutil/5.25 None application Utility Command-line interface for Google Cloud Platform products and services
gtdbtk 0.1.3 gtdbtk/0.1 None application computational biology A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gtdbtk 1.3.0 gtdbtk/1.3 None application computational biology A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gtdbtk 1.5.0 gtdbtk/1.5 None application computational biology A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gubbins 2.3.4 gubbins/2.3 None application Biology Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
gubbins 3.1.6 gubbins/3.1 None application Biology Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
guppy 6.2.1 guppy/6.2 None application Bioinformatics Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy 6.3.4 guppy/6.3 None application Bioinformatics Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy 6.5.7 guppy/6.5 None application Bioinformatics Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy-gpu 6.2.1 guppy-gpu/6.2 None application Bioinformatics Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy-gpu 6.3.4 guppy-gpu/6.3 None application Bioinformatics Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy-gpu 6.5.7 guppy-gpu/6.5 None application Bioinformatics Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
gurobi 10.0.2 gurobi/py39/10.0 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi 10.0.2 gurobi/py310/10.0 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi 11.0.0 gurobi/py39/11.0 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi 11.0.0 gurobi/py310/11.0 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi 9.0.3 gurobi/py36/9.0 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi 9.0.3 gurobi/py37/9.0 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi 9.5.1 gurobi/py38/9.5 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi 9.5.1 gurobi/py39/9.5 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python 8.1.0 gurobi-python/py27/8.1 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python 8.1.0 gurobi-python/py35/8.1 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python 8.1.0 gurobi-python/py36/8.1 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
halla 0.8.17 halla/0.8 None application computational biology HAllA: Hierarchically All-against-All Association Testing.
hapflk 1.3.0 hapflk/1.3 None application package hapflk is a software implementing the hapFLK [1] and FLK [2] tests for the detection of selection signatures based on multiple population genotyping data.
hapsolo 2021.10.09 hapsolo/2021.10.09 None application computational biology An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding.
haptools 0.4.0 haptools/0.4 None application bioinformatics Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
haskell-platform 8.2.1 haskell-platform/8.2.1 None application Utilities The Haskell Platform is a collection of software packages, tools and libraries that create a common platform for using and developing applications in Haskell..
haslr 0.8a1 haslr/0.8a1 None application genomics A fast tool for hybrid genome assembly of long and short reads
hdf-eos2 2.20 hdf-eos2/2.20 compiler/pgi/20 compiler/intel/19 compiler/gcc/10 compiler/gcc/9 compiler/intel/20 library runtime support
hdf4 4.2.15 hdf4/4.2 compiler/pgi/20 compiler/intel/19 compiler/intel/20 compiler/gcc/10 compiler/gcc/9 library runtime support
hdf5 1.12 hdf5/1.12 compiler/gcc/11 compiler/intel/19 compiler/intel/18 compiler/gcc/10 compiler/intel/20 compiler/gcc/9 compiler/pgi/20 library runtime support
hdf5 1.8 hdf5/1.8 compiler/intel/18 compiler/gcc/9 None library runtime support
hiddendomains 2.3 hiddendomains/2.3 None application chip-seq hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains.
hifiasm 0.19.8 hifiasm/0.19 None application computational biology Haplotype-resolved assembler for accurate Hifi reads
hisat2 2.0.5 hisat2/2.0 None application computational biology graph-based alignment of next generation sequencing reads to a population of genomes
hisat2 2.1.0 hisat2/2.1 None application computational biology graph-based alignment of next generation sequencing reads to a population of genomes
hisat2 2.2.1 hisat2/2.2 None application computational biology graph-based alignment of next generation sequencing reads to a population of genomes
hmmer 3.3.1 hmmer/3.3 compiler/gcc/9:openmpi/4.0 compiler/gcc/11:openmpi/4.1 application computational biology HMMER biosequence analysis using profile hidden Markov models
homer 4.11 homer/4.11 None application computational biology Software for motif discovery and next generation sequencing analysis
hotspot3d 0.6.0 hotspot3d/0.6 None application bioinformatics This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed.
htseq 0.11.2 htseq/py27/0.11 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.11.2 htseq/py36/0.11 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.11.2 htseq/py37/0.11 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.13.5 htseq/py36/0.13 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.13.5 htseq/py39/0.13 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.5.4p5 htseq/0.5.4p5 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.6.1p1 htseq/0.6.1p1 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.9.1 htseq/0.9 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 2.0.5 htseq/py39/2.0 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 2.0.5 htseq/py310/2.0 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htslib 1.12.2 htslib/1.12 compiler/intel/19 compiler/gcc/10 compiler/intel/20 compiler/gcc/9 application computational biology HTSlib is an implementation of a unified C library for accessing common file formats.
htslib 1.3.2 htslib/1.3 None application computational biology HTSlib is an implementation of a unified C library for accessing common file formats.
htslib 1.7 htslib/1.7 None application computational biology HTSlib is an implementation of a unified C library for accessing common file formats.
htstream e919d21 htstream/e919d21 None application Bioinformatics A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes.
humann 3.0.0 humann/3.0 None application computational biology HUMAnN 3 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.
humann 3.1.1 humann/3.1 None application computational biology HUMAnN 3 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.
humann 3.6 humann/3.6 None application computational biology HUMAnN 3 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.
humann2 0.11.2 humann2/0.11 None application computational biology HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
humann2 0.9.9 humann2/0.9 None application computational biology HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
humann2 2.8.1 humann2/2.8 None application computational biology HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
i-pi 2.4.0 i-pi/py39/2.4 None application molecular dynamics i-PI: a universal force engine
ibm-ilog-cplex 12.10 ibm-ilog-cplex/12.10 None application iIBM ILOG CPLEX Optimization Studio
ibm-ilog-cplex 20.10 ibm-ilog-cplex/20.10 None application iIBM ILOG CPLEX Optimization Studio
ibm-ilog-cplex 22.1.0 ibm-ilog-cplex/22.1.0 None application iIBM ILOG CPLEX Optimization Studio
icount 2.0.0 icount/py36/2.0 None application Bioinformatics Computational pipeline for analysis of iCLIP data
icount 2.0.0 icount/py37/2.0 None application Bioinformatics Computational pipeline for analysis of iCLIP data
idba 1.1.3 idba/1.1 None application computational biology IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.
idr 2.0 idr/2.0 None application computational biology The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.
igs-portal-client 1.4.4 igs-portal-client/1.4 None application System Python-based client for downloading data made available through portals powered by the GDC-based portal system.
igvtools 2.14.1 igvtools/2.14 None application genomics Command line tools for IGV
igvtools 2.16.2 igvtools/2.16 None application genomics Command line tools for IGV
igvtools 2.5.3 igvtools/2.5 None application genomics Command line tools for IGV
ilastik 1.3.3post3 ilastik/1.3 None application Image Processing ilastik is a gui driven open source interactive image classification, segmentation and analysis tool that uses machine learning.
ilastik 1.4.0.post1 ilastik/1.4 None application Image Processing ilastik is a gui driven open source interactive image classification, segmentation and analysis tool that uses machine learning.
ilastik-gpu 1.4.0.post1 ilastik-gpu/1.4 None application Image Processing ilastik is a gui driven open source interactive image classification, segmentation and analysis tool that uses machine learning.
ima3 1.0 ima3/1.0 None application Phylogeny IMa3 provides for estimation of the posterior probability of the population phylogenetic topology by using a new kind of data augmentation called a 'hidden genealogy'.
imagemagick 7.0.8_10 imagemagick/7.0 None application bitmap Software suite to create, edit, compose, or convert bitmap images.
imagemagick 7.1.0_2 imagemagick/7.1 None application bitmap Software suite to create, edit, compose, or convert bitmap images.
imbalanced-learn-gpu 0.4.3 imbalanced-learn-gpu/py36/0.4 None application Machine Learning Python module to balance data set using under- and over-sampling
imbalanced-learn-gpu 0.4.3 imbalanced-learn-gpu/py37/0.4 None application Machine Learning Python module to balance data set using under- and over-sampling
impute2 2.3.2 impute2/2.3 None application computational biology IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes.
instrain 1.3.7 instrain/1.3 None application bioinformatics Calculation of strain-level metrics
intel-mkl 12 intel-mkl/12 None library tools Numerical library, contains blas/lapack
intel-mkl 13 intel-mkl/13 None library tools Numerical library, contains blas/lapack
intel-mkl 15 intel-mkl/15 None library tools Numerical library, contains blas/lapack
intel-mkl 16 intel-mkl/16 None library tools Numerical library, contains blas/lapack
intel-mkl 18 intel-mkl/18 None library tools Numerical library, contains blas/lapack
intel-mkl 19 intel-mkl/19 None library tools Numerical library, contains blas/lapack
intel-mkl 20 intel-mkl/20 None library tools Numerical library, contains blas/lapack
intel-mkl 2021.1 intel-mkl/2021.1 None library tools Numerical library, contains blas/lapack
intel-mkl 2022.0 intel-mkl/2022.0 None library tools Numerical library, contains blas/lapack
intel-mpi 18 intel-mpi/18 compiler/intel/18 library runtime support
intel-mpi 19 intel-mpi/19 compiler/intel/19 library runtime support
intel-mpi 2021 intel-mpi/2021 compiler/intel/2021 library runtime support
intel-tbb 2021.13 intel-tbb/2021.13 None library runtime support
intel-tbb 2021.2 intel-tbb/2021.2 None library runtime support
intel-tbb 2021.5 intel-tbb/2021.5 None library runtime support
interproscan 5.52-86.0 interproscan/5.52 None application computational biology Scans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan 5.63-95.0 interproscan/5.63 None application computational biology Scans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan 5.69-101.0 interproscan/5.69 None application computational biology Scans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan 5.8-49.0 interproscan/5.8 None application computational biology Scans a range of protein signatures against your sequences and provides protein functional analysis.
ipr-support 1.0 ipr-support/1.0 None application computational biology Support environment containing a few small libraries for InterProScan. Not useful as a stand-alone environment.
iqtree 1.6.7 iqtree/1.6 None application computational biology IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.
iqtree 2.2.2.7 iqtree/2.2 None application computational biology IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.
iqtree 2.3.4 iqtree/2.3 None application computational biology IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.
irods 4.1 irods/4.1 None None application unknown The integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only.
irods 4.2 irods/4.2 None application unknown The integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only.
itk 5.2.0 itk/py37/5.2 None application Utility ITK is an open-source toolkit for multidimensional image analysis
itk 5.2.0 itk/py38/5.2 None application Utility ITK is an open-source toolkit for multidimensional image analysis
itk 5.2.0 itk/py39/5.2 None application Utility ITK is an open-source toolkit for multidimensional image analysis
ivar 1.4.2 ivar/1.4 None application computational biology iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
jags 4.3 jags/4.3 compiler/intel/2021 compiler/gcc/11 application mathematics JAGS is Just Another Gibbs Sampler.
jamm 1.0.7r2 jamm/1.0.7r2 None application computational biology JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately.
jasper 1.9 jasper/1.9 compiler/pgi/20 library runtime support A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
jasper 1.900.22 jasper/1.900.22 compiler/pgi/20 library runtime support A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
jasper 2.0 jasper/2.0 compiler/pgi/20 compiler/intel/20 compiler/gcc/10 compiler/intel/19 compiler/gcc/9 library runtime support A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
jasper 4.0.0 jasper/4.0 None library runtime support A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
java 1.6 java/1.6 None application system OpenJDK (Java).
java 1.7 java/1.7 None application system OpenJDK (Java).
java 1.8 java/1.8 None application system OpenJDK (Java).
java 11 java/11 None application system OpenJDK (Java).
java 12 java/12 None application system OpenJDK (Java).
java 17 java/17 None application system OpenJDK (Java).
java 19 java/19 None application system OpenJDK (Java).
jellyfish 2.2.0 jellyfish/2.2 None application Biology Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence
jellyfish 2.3.0 jellyfish/2.3 None application Biology Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence
jmosaics 1.10 jmosaics/1.10 None application computational biology Joint analysis of multiple ChIP-Seq data sets.
jpeg 9e jpeg/9e compiler/pgi/20 compiler/gcc/11 compiler/intel/19 compiler/gcc/9 compiler/intel/20 compiler/gcc/10 library runtime support
jq 1.6 jq/1.6 None application Utility A command-line JSON processor.
juicer 1.6 juicer/1.6 None application computational biology A One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
julia 0.6.2 julia/0.6 None application Language A high-performance dynamic programming language for data science
julia 1.0 julia/1.0 None application Language A high-performance dynamic programming language for data science
julia 1.1.1 julia/1.1 None application Language A high-performance dynamic programming language for data science
julia 1.10.2 julia/1.10 None application Language A high-performance dynamic programming language for data science
julia 1.6.1 julia/1.6 None application Language A high-performance dynamic programming language for data science
julia 1.7.2 julia/1.7 None application Language A high-performance dynamic programming language for data science
julia 1.9.2 julia/1.9 None application Language A high-performance dynamic programming language for data science
jupyter-book 0.15.1 jupyter-book/0.15 None application Publishing Jupyter Book: Create an online book with Jupyter Notebooks
justorthologs 0.0.20190308 justorthologs/0.0.20190308 None application Biology JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.
jvarkit 2024.04.20 jvarkit/2024.04.20 None application bioinformatics Java Java utilities for Bioinformatics.
jvarkit-msa2vcf 1.0 jvarkit-msa2vcf/1.0 None application computational biology Getting a VCF file from a CLUSTAW or a FASTA alignment.
jvarkit-sam2tsv 1.0 jvarkit-sam2tsv/1.0 None application computational biology Prints the SAM alignments as a TAB delimited file.
jvarkit-vcf2bam 2018.04.05 jvarkit-vcf2bam/2018.04.05 None application computational biology Converts VCF to BAM files
jwt-cli 3.3.0 jwt-cli/3.3 None application json A super fast CLI tool to decode and encode JWTs built in Rust.
kaiju 1.10.0 kaiju/1.10 None application Bioinformatics Fast and sensitive taxonomic classification for metagenomics
kaiju 1.7.3 kaiju/1.7 None application Bioinformatics Fast and sensitive taxonomic classification for metagenomics
kaiju 1.8.2 kaiju/1.8 None application Bioinformatics Fast and sensitive taxonomic classification for metagenomics
kalign 2.0 kalign/2.0 None application computational biology Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
kalign 2.03 kalign/2.03 None application computational biology Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
kallisto 0.46.2 kallisto/0.46 None application computational biology Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
kat 2.4.0 kat/2.4 None application bioinformatics KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts
keras 2.2.4 keras/py27/2.2 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.2.4 keras/py36/2.2 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.3.1 keras/py27/2.3 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.3.1 keras/py36/2.3 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.4.3 keras/py37/2.4 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.4.3 keras/py38/2.4 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.6.0 keras/py38/2.6 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.6.0 keras/py39/2.6 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.2.4 keras-gpu/py27/2.2 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.2.4 keras-gpu/py36/2.2 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.3.1 keras-gpu/py27/2.3 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.3.1 keras-gpu/py36/2.3 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.4.3 keras-gpu/py37/2.4 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.4.3 keras-gpu/py38/2.4 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.6.0 keras-gpu/py38/2.6 None application machine learning Deep Learning Library for Theano and TensorFlow
keras-gpu 2.6.0 keras-gpu/py39/2.6 None application machine learning Deep Learning Library for Theano and TensorFlow
khmer 2.0 khmer/2.0 None application computational biology Khmer is tools for in-memory nucleotide sequence k-mer counting, filtering, graph traversal and more.
kmc 3.1.1 kmc/3.1 None application computational biology Tools for efficient k-mer counting and filtering of reads based on k-mer content
kneaddata 0.10.0 kneaddata/0.10 None application computational biology KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
kneaddata 0.12.0 kneaddata/0.12 None application computational biology KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
kneaddata 0.7.2 kneaddata/0.7 None application computational biology KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
kraken 1.0 kraken/1.0 None application computational biology Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
kraken2 2.0.8-beta kraken2/2.0.8-beta None application Bioinformatics Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
kraken2 2.1.3 kraken2/2.1 None application Bioinformatics Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
krona 2.7.1 krona/2.7 None application bioinformatics Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
kronos 2.3.0 kronos/2.3 None application workflow Kronos is a highly flexible Python-based software tool that mainly enables bioinformatics developers, i.e. bioinformaticians who develop workflows for analyzing genomic data, to quickly make a workflow.
ksnp 3.1 ksnp/3.1 None application computational biology kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.
lammps 07Aug2019 lammps/07Aug2019 compiler/gcc/11:openmpi/4.1 library runtime support
lammps 23Jun2022 lammps/23June2022 compiler/gcc/11:openmpi/4.1 library runtime support
lammps 27June2024 lammps/27June2024 compiler/intel/20:openmpi/4.1 compiler/gcc/11:openmpi/4.1 library runtime support
lammps 29Sep2021 lammps/29Sep2021 compiler/gcc/11:openmpi/4.1 compiler/gcc/10:openmpi/4.0 compiler/intel/20:openmpi/4.1 compiler/intel/19:openmpi/4.0 compiler/gcc/10:openmpi/4.1 library runtime support
lammps 2Aug2023 lammps/2Aug2023 compiler/gcc/11:openmpi/4.1 compiler/intel/20:openmpi/4.1 library runtime support
lapack 3.9.1 lapack/3.9 compiler/intel/18 compiler/intel/20 compiler/gcc/9 compiler/gcc/11 compiler/gcc/10 compiler/pgi/20 compiler/intel/19 application Utility LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
lasagne 0.1 lasagne/py27/0.1 None application neural networks A lightweight library to build and train neural networks in Theano
lasagne 0.1 lasagne/py36/0.1 None application neural networks A lightweight library to build and train neural networks in Theano
lastools v2.0.2 lastools/2.0 None application Geoscience LASlib and LASzip libraries plus open source utilities from LAStools for manipulating LiDAR data in LAS format
lastz 1.04.22 lastz/1.04 None application computational biology LASTZ is a program for aligning DNA sequences, a pairwise aligner.
lcms2 2.13.1 lcms2/2.13 compiler/intel/20 compiler/pgi/20 compiler/intel/19 compiler/gcc/9 compiler/gcc/10 library runtime support
lefse 1.0.8.post1 lefse/1.0 None application computational biology LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
lefse 1.1.2 lefse/1.1 None application computational biology LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
lftp 4.8.3 lftp/4.8 None application system LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
lftp 4.9.1 lftp/4.9 None application system LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
libbeef 0.1.3 libbeef/0.1 compiler/intel/19 compiler/gcc/9 compiler/intel/20 compiler/pgi/20 compiler/gcc/10 application Physics
libgeotiff 1.6.0 libgeotiff/1.6 compiler/intel/19 compiler/gcc/10 compiler/intel/20 compiler/gcc/9 compiler/pgi/20 library runtime support
libidn 1.36 libidn/1.36 compiler/intel/19 library runtime support
libint 2.6.0 libint/2.6 compiler/intel/20 library runtime support
libjpeg 2.0.5 libjpeg/2.0 compiler/pgi/20 compiler/gcc/11 compiler/gcc/9 compiler/gcc/10 compiler/intel/20 compiler/intel/19 library runtime support
libpng 1.6.37 libpng/1.6 compiler/pgi/20 compiler/gcc/10 compiler/gcc/11 compiler/intel/19 compiler/intel/20 compiler/gcc/9 library runtime support
libtiff 4.1.0 libtiff/4.1 compiler/gcc/11 compiler/gcc/9 compiler/intel/19 compiler/gcc/10 compiler/pgi/20 compiler/intel/20 library runtime support
libwebp 1.1.0 libwebp/1.1 compiler/intel/19 compiler/gcc/10 compiler/pgi/20 compiler/intel/20 compiler/gcc/11 compiler/gcc/9 library runtime support
libxc 5.1.6 libxc/5.1 compiler/intel/20 compiler/pgi/20 compiler/gcc/10 compiler/intel/19 compiler/gcc/9 library runtime support
libxc 5.2.0 libxc/5.2 compiler/gcc/9 compiler/gcc/10 compiler/intel/20 compiler/pgi/20 compiler/intel/19 library runtime support
libxml2 2.9.9 libxml2/2.9 compiler/intel/20 compiler/intel/18 compiler/pgi/20 compiler/intel/19 compiler/gcc/10 compiler/gcc/9 library runtime support
libxsmm 1.17 libxsmm/1.17 compiler/intel/20 library runtime support
lmdb 0.9 lmdb/0.9 None library unknown Lightning memory-mapped database library.
lmod None lmod None unknown unknown Lmod: An Environment Module System
lmod lmod lmod/lmod None unknown unknown Lmod: An Environment Module System
lofreq 2.1.3.1 lofreq/2.1 None application computational biology LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.
logomaker 0.8 logomaker/py27/0.8 None application Utility Package for making Sequence Logos
logomaker 0.8 logomaker/py36/0.8 None application Utility Package for making Sequence Logos
ls-bsr 0.0.2022.11.15 ls-bsr/2022.11.15 None application bioinformatics Large scale Blast Score Ratio (BSR) analysis.
lsdyna 12.0.0 lsdyna/12 None unknown unknown
lsdyna 13.1.1 lsdyna/13.1 None unknown unknown
lsdyna 14.0.0 lsdyna/14.0 None unknown unknown
lynx 2.8.8 lynx/2.8 None application tool Lynx is a text browser for the World Wide Web.
lyve-set 2.0.1 lyve-set/2.0 None application computational biology LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.
m4 1.0 m4/1.4 None application Utilities The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
maaslin 0.0.5 maaslin/0.05 None application computational biology MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and microbial community abundance or function.
maaslin2 0.3.0 maaslin2/0.3 None application computational biology MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.
maaslin2 0.99.12 maaslin2/0.99 None application computational biology MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.
macs2 2.1.1 macs2/2.1 None application computational biology MACS -- Model-based Analysis of ChIP-Seq
macs2 2.2.9 macs2/2.2 None application computational biology MACS -- Model-based Analysis of ChIP-Seq
macs3 3.0.2 macs3/3.0 None application computational biology MACS -- Model-based Analysis of ChIP-Seq
maestro 1.5.1 maestro/1.5 None application computational biology MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake.
mafft 7.149 mafft/7.149 None application Bioinformatics Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
mafft 7.407 mafft/7.407 None application Bioinformatics Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
mafft 7.520 mafft/7.520 None application Bioinformatics Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
mafft 7.526 mafft/7.526 None application Bioinformatics Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
magicblast 1.7.0 magicblast/1.7 None application computational biology NCBI BLAST next generation read mapper
make 1.0 make/4.3 None application Utilities The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
maker 2.31.10 maker/2.31 None application computational biology MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms.
maker 3.01.03 maker/3.01 None application computational biology MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms.
mamba 0.13.0 mamba/0.13 None application system
mamba 0.15.3 mamba/0.15 None application system
mamba 0.5.1 mamba/0.5.1 None application system
mamba 0.7.3 mamba/0.7 None application system
mamba 23.1.0/1.3.1 mamba/1.3 None application system
mamba 23.11.0/1.5.4 mamba/1.5 None application system
mamba 23.7.2/1.4.9 mamba/1.4 None application system
mamba 4.12.0/0.24.0 mamba/0.24 None application system
manta 1.6.0 manta/1.6 None application Structural variant Structural variant and indel caller for mapped sequencing data
mapping-iterative-assembler 1.0 mapping-iterative-assembler/1.0 None application bioinformatics Consensus calling or `reference assisted assembly`, chiefly of ancient mitochondria.
mapsplice 2.2.0 mapsplice/2.2 None application computational biology MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.
maq 0.7 maq/0.7 None application computational biology maq - Mapping and Assembly with Quality.
mash 2.2.2 mash/2.2 None application computational biology Fast sequence distance estimator that uses MinHash
mashmap 2.0 mashmap/2.0 None application computational biology A fast approximate aligner for long DNA sequences
mashmap 3.1.1 mashmap/3.1 None application computational biology A fast approximate aligner for long DNA sequences
mashtree 1.4.6 mashtree/1.4 None application computational biology Create a tree using Mash distances
masurca 3.3.1 masurca/3.3 None application Biology MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
masurca 4.0.9 masurca/4.0 None application Biology MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
masurca 4.1.0 masurca/4.1 None application Biology MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
mathematica 11.0 mathematica/11.0 None application Engineering
mathematica 11.3 mathematica/11.3 None application Engineering
mathematica 12.0 mathematica/12.0 None application Engineering
mathematica 12.3 mathematica/12.3 None application Engineering
mathematica 13.1 mathematica/13.1 None application Engineering
mathematica 13.2 mathematica/13.2 None application Engineering
matio 1.5 matio/1.5 compiler/gcc/10 library runtime support
matlab r2012b matlab/r2012b None unknown unknown
matlab r2013b matlab/r2013b None unknown unknown
matlab r2014b matlab/r2014b None unknown unknown
matlab r2015b matlab/r2015b None unknown unknown
matlab r2016a matlab/r2016a None unknown unknown
matlab r2016b matlab/r2016b None unknown unknown
matlab r2017a matlab/r2017a None unknown unknown
matlab r2017b matlab/r2017b None unknown unknown
matlab r2018a matlab/r2018a None unknown unknown
matlab r2018b matlab/r2018b None unknown unknown
matlab r2019a matlab/r2019a None unknown unknown
matlab r2019b matlab/r2019b None unknown unknown
matlab r2020a matlab/r2020a None unknown unknown
matlab r2020b matlab/r2020b None unknown unknown
matlab r2021a matlab/r2021a None unknown unknown
matlab r2021b matlab/r2021b None unknown unknown
matlab r2022a matlab/r2022a None unknown unknown
matlab r2022b matlab/r2022b None unknown unknown
matlab r2023a matlab/r2023a None unknown unknown
matlab r2023b matlab/r2023b None unknown unknown
matlab r2024a matlab/r2024a None unknown unknown
mauve 2.4 mauve/2.4 None application computational biology mauve - Multiple Genome Alignment.
maven 3.2 maven/3.2 None application system Apache Maven is a software project management and comprehension tool.
maven 3.5 maven/3.5 None application system Apache Maven is a software project management and comprehension tool.
maxbin2 2.2.7 maxbin2/2.2 None application Biology MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
maxquant 1.6.10.43 maxquant/1.6 None application biochemistry MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
maxquant 2.0.3.0 maxquant/2.0 None application biochemistry MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
mbuffer 20171011 mbuffer/20171011 None application buffer Mbuffer is a tool for buffering data streams with a large set of unique features.
mcl 14.137 mcl/14.137 None application computational biology MCL
medaka 1.7.2 medaka/py38/1.7 None application bioinformatics Neural network sequence error correction.
medaka-gpu 1.7.2 medaka-gpu/py38/1.7 None application bioinformatics Neural network sequence error correction.
meep 1.3 meep/1.3 None library runtime support
meerkat 0.189 meerkat/0.1 None application computational biology Meerkat is designed to identify structural variations
megahit 1.1 megahit/1.1 None application computational biology MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
megahit 1.2.9 megahit/1.2 None application computational biology MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
megahit-gpu 1.1 megahit-gpu/1.1 None application computational biology MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
megalodon 2.4.1 megalodon/2.4 None application Genomics Nanopore modified base and sequence variant detection.
megalodon 2.5.0 megalodon/2.5 None application Genomics Nanopore modified base and sequence variant detection.
megalodon-gpu 2.5.0 megalodon-gpu/2.5 None application Bioinformatics Nanopore modified base and sequence variant detection.
megan 6.12.3 megan/6.12 None application Computational Biology A tool for studying the taxonomic content of a set of DNA reads
megan 6.25.9 megan/6.25 None application Computational Biology A tool for studying the taxonomic content of a set of DNA reads
melonnpan 2019.03.22 melonnpan/2019.03.22 None application computational biology MelonnPan is a computational method for predicting metabolite compositions from shotgun metagenomic sequencing data.
merqury 1.3 merqury/1.3 None application Genome Analysis Evaluate genome assemblies with k-mers and more.
meryl 1.4.1 meryl/1.4 None application genome analysis A genomic k-mer counter (and sequence utility) with nice features
meson 0.61.1 meson/0.61 None application Utilities The Meson Build System
metabat2 2.15 metabat2/2.15 None application computational biology Metagenome binning
metabolic 20210303 metabolic/20210303 None application Bioinformatics A scalable high-throughput metabolic and biogeochemical functional trait profiler.
metacv 2.3.0 metacv/2.3 None application Bioinformatics Composition based classification for short metagenomic sequences
metaphlan 1.7 metaphlan/1.7 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan 3.0.3 metaphlan/3.0 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan 3.1.0 metaphlan/3.1 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan 4.0.6 metaphlan/4.0 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2 2.6.0 metaphlan2/2.6 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2 2.7.8 metaphlan2/2.7 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2 2.96.1 metaphlan2/2.96 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metasnv 2.0.1 metasnv/2.0 None application Biology SNV calling software
metasv 0.5.4 metasv/0.5 None application computational biology An accurate and integrative structural-variant caller for next generation sequencing.
metavelvet 1.2.01 metavelvet/1.2 None application computational biology MetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
metawrap 1.1 metawrap/1.1 None application computational biology MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metawrap 1.2 metawrap/1.2 None application computational biology MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metawrap 1.3.2 metawrap/1.3 None application computational biology MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metaxa2 2.2.3 metaxa2/2.2 None application classification Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.
methylpy 1.4.1 methylpy/py27/1.4 None application bioinformatics Bisulfite sequencing data processing and differential methylation analysis
methylpy 1.4.1 methylpy/py36/1.4 None application bioinformatics Bisulfite sequencing data processing and differential methylation analysis
methylpy 1.4.1 methylpy/py37/1.4 None application bioinformatics Bisulfite sequencing data processing and differential methylation analysis
metis 4.0.0 metis/4.0 compiler/gcc/9 library runtime support
metis 5.1.0 metis/5.1 compiler/gcc/9 compiler/pgi/20 compiler/intel/19 compiler/intel/20 compiler/gcc/10 library runtime support
mfold 3.6 mfold/3.6 None application computational biology Mfold web server for nucleic acid folding and hybridization prediction.
mgblast 2.2.14 mgblast/2.2 None application Alignment fast all-vs-all DNA alignment tool, modification of megablast from a 2006 version of NCBI C Toolkit
mgltools 1.5.7 mgltools/1.5 None application computational structural biology MGLTools is an program for visualization and analisys of molecular structures.
miRDeep 2.0.0 miRDeep/2.0 None application computational biology miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
micropita 1.1.0 micropita/1.1 None application computational biology microPITA is a computational tool enabling sample selection in two-stage (tiered) studies.
midas 1.3.2 midas/1.3 None application computational biology An integrated pipeline for estimating strain-level genomic variation from metagenomic data
midnight-commander 4.8.22 midnight-commander/4.8 None application Utility GNU Midnight Commander is a visual file manager, licensed under GNU General Public License and therefore qualifies as Free Software. It's a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Internal viewer and editor are included.
minibusco 0.2.1 minibusco/0.2 None application bioinformatics minibusco: a faster and more accurate reimplementation of BUSCO
miniforge 24.5.0/1.5.8 miniforge/24.5 None application system
minimap2 2.16 minimap2/2.16 None application bioinformatics A versatile pairwise aligner for genomic and spliced nucleotide sequences.
minimap2 2.26 minimap2/2.26 None application bioinformatics A versatile pairwise aligner for genomic and spliced nucleotide sequences.
minpack 19961126 minpack/19961126 compiler/gcc/9 compiler/intel/20 compiler/pgi/20 compiler/gcc/10 compiler/intel/19 application Utility Minpack includes software for solving nonlinear equations and nonlinear least squares problems.
miranda 3.3a miranda/3.3a None application computational biology An algorithm for finding genomic targets for microRNAs
misis 1.0 misis/1.0 None application computational biology
mitosalt 1.1.1 mitosalt/1.1 None application computational biology Identification of mitochondrial structural alterations.
mitoz 3.6 mitoz/3.6 None application computational biology MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
mldata 1.0 mldata/1.0 None application computer science Static data resources for machine-learning/AI.
mlflow 2.16.2 mlflow/py310/2.16 None application machine learning MLflow is an open source platform for the machine learning lifecycle.
mlflow 2.16.2 mlflow/py312/2.16 None application machine learning MLflow is an open source platform for the machine learning lifecycle.
mlpack 2.2.5 mlpack/2.2 None application Machine Learning mlpack a fast, flexible machine learning library
mlpack 3.0.3 mlpack/3.0 None application Machine Learning mlpack a fast, flexible machine learning library
mlst 2.16.2 mlst/2.16 None application computational biology Scan contig files against PubMLST typing schemes
mlst 2.19.0 mlst/2.19 None application computational biology Scan contig files against PubMLST typing schemes
mlst 2.22.0 mlst/2.22 None application computational biology Scan contig files against PubMLST typing schemes
mmseqs2 13.45111 mmseqs2/13.45111 compiler/gcc/9:openmpi/4.0 compiler/gcc/10:openmpi/4.0 compiler/gcc/11:openmpi/4.1 application Bioinformatics MMseqs2: ultra fast and sensitive search and clustering suite.
modeller 9.19 modeller/9.19 None unknown unknown
modflow-2005 1.12.00 modflow-2005/1.12 None application USGS Three-dimensional finite-difference ground-water flow model.
mongodb-client 3.2 mongodb-client/3.2 None application Utility Client programs for MongoDB.
mongodb-client 3.4 mongodb-client/3.4 None application Utility Client programs for MongoDB.
mongodb-client 4.2 mongodb-client/4.2 None application Utility Client programs for MongoDB.
mono 4.6 mono/4.6 None application compiler Mono is a software platform designed to allow developers to easily create cross platform applications.
mono 5.10 mono/5.10 None application compiler Mono is a software platform designed to allow developers to easily create cross platform applications.
mono 5.14.0.177 mono/5.14 None application compiler Mono is a software platform designed to allow developers to easily create cross platform applications.
morgan 3.4 morgan/3.4 None application computational biology MORGAN is part of our software for Markov chain Monte Carlo in Genetic Analysis.
mosaik 2.2 mosaik/2.2 None application computational biology MOSAIK is a reference-guided aligner for next-generation sequencing technologies.
mosdepth 0.2.4 mosdepth/0.2 None application computational biology Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.
mosdepth 0.3.8 mosdepth/0.3 None application computational biology Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.
mothur 1.41.3 mothur/1.41 None application Bioinformatics This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mothur 1.45.3 mothur/1.45 None application Bioinformatics This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mothur 1.46.1 mothur/1.46 None application Bioinformatics This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mpfr 4.1.0 mpfr/4.1 compiler/gcc/10 library runtime support The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
mpich 3.4 mpich/3.4 compiler/gcc/9 library runtime support
mpich 4.0 mpich/4.0 compiler/gcc/10 library runtime support
mpich2 1.5 mpich2/1.5 compiler/gcc/9 library runtime support
mplus 6.12 mplus/6.12 None application unknown Mplus is a latent variable modeling program with a wide variety of analysis capabilities.
mplus 7.0 mplus/7.0 None application unknown Mplus is a latent variable modeling program with a wide variety of analysis capabilities.
mrbayes 3.2.7 mrbayes/3.2 None application computational biology Bayesian Inference of Phylogeny
mridata 1.0 mridata/1.0 None application brain imaging Static data resources for MRI/NeuroImaging.
mrtrix3 3.0.3 mrtrix3/3.0 None application computational neuroimaging Advanced tools for the analysis of diffusion MRI data.
mrtrix3tissue 5.2.9 mrtrix3tissue/5.2 None application computational neuroimaging MRtrix3Tissue adds capabilities for 3-Tissue CSD modelling and analysis to a complete version of MRtrix3.
msgf_plus 2020.06.22 msgf_plus/2020.06.22 None application proteomics MS-GF+ is a new MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).
mspkmercounter 0.10.0 mspkmercounter/0.10 None application Biology MSPKmerCounter is a k-mer counter based on the minimum substring partitioning technique.
mugsy 1.2.3 mugsy/1.2 None application computational biology Mugsy is a multiple whole genome aligner.
mujoco 2.1.0 mujoco/2.1 None application Simulation MuJoCo | advanced physics simulation.
mujoco 200 mujoco/200 None application Simulation MuJoCo | advanced physics simulation.
multigps 0.74 multigps/0.74 None application computational biology MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions.
multiqc 0.8 multiqc/py27/0.8 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 0.8 multiqc/py35/0.8 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 1.6 multiqc/py27/1.6 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 1.6 multiqc/py35/1.6 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 1.6 multiqc/py36/1.6 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 1.8 multiqc/py27/1.8 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 1.8 multiqc/py37/1.8 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiwfn 3.8 multiwfn/3.8 compiler/intel/18 application Wavefunction Multiwfn is a powerful program for realizing electronic wavefunction analysis, which is a key ingredient of quantum chemistry.
mumax3 3.10 mumax3/3.10 None application micromagnetics GPU-accelerated micromagnetic simulator
mumax3 3.9.3 mumax3/3.9 None application micromagnetics GPU-accelerated micromagnetic simulator
mummer 3.23 mummer/3.23 None application bioinformatics MUMmer is a system for rapidly aligning entire genomes
mummer4 4.0.0beta2 mummer4/4.0 None application Bioinformatics MUMmer is a system for rapidly aligning entire genomes
muscle 3.8.1551 muscle/3.8 None application computational biology MUSCLE: multiple sequence alignment with high accuracy and high throughput
muscle 5.1 muscle/5.1 None application computational biology MUSCLE: multiple sequence alignment with high accuracy and high throughput
music 1.0 music/1.0 None application computational biology MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
mutect 1.1 mutect/1.1 None application computational biology MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
mxnet 0.9.3a mxnet/0.9.3 None application AI MXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices.
mxnet 1.5.0 mxnet/1.5 None application AI MXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices.
mysql-client 8.0.23 mysql-client/8.0 None application Database MySQL client applications and tools
mytaxa 1.0 mytaxa/1.0 None application computational biology MyTaxa - Assign taxonomy to metagenomic fragments.
nano 2.9.8 nano/2.9 None application Utility Nano's ANOther editor, an enhanced free Pico clone
nano 5.5 nano/5.5 None application Utility Nano's ANOther editor, an enhanced free Pico clone
nano 5.7 nano/5.7 None application Utility Nano's ANOther editor, an enhanced free Pico clone
nano 6.2 nano/6.2 None application Utility Nano's ANOther editor, an enhanced free Pico clone
nano 8.2 nano/8.2 None application Utility Nano's ANOther editor, an enhanced free Pico clone
nanofilt 2.8.0 nanofilt/2.8 None application Bioinformatics Filtering and trimming of Oxford Nanopore Sequencing data
nanoplot 1.40.2 nanoplot/1.40 None application computational biology Plotting suite for long read sequencing data and alignments
nanopolish 0.14.0 nanopolish/0.14 None application bioinformatics Signal-level algorithms for MinION data.
ncbi-amrfinderplus 3.8.4 ncbi-amrfinderplus/3.8 None application bioinformatics AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
ncbi-datasets-cli 16.4.4 ncbi-datasets-cli/16.4 None application bioinformatics NCBI Datasets command-line clients
ncbi-download 0.2.6 ncbi-download/0.2 None application computational biology Python scriopt for downloading bacterial and fungal genomes from NCBI.
ncbi-download 0.3.3 ncbi-download/0.3 None application computational biology Python scriopt for downloading bacterial and fungal genomes from NCBI.
ncdu 1.15 ncdu/1.15 None application System NCurses Disk Usage
ncl 6.6.2 ncl/6.6 None application utility NCAR Command Language
nco 4.8.1 nco/4.8 None library runtime support Suite of programs for manipulating NetCDF/HDF4 files.
ncview 2.1.7 ncview/2.1 compiler/pgi/20 compiler/intel/20 library runtime support Ncview is a visual browser for netCDF format files.
nda-tools 0.2.23 nda-tools/0.2 None application NDA web services Python package for interacting with NDA web services.
neper 3.3.0 neper/3.3 None application Applications Neper is a software package for polycrystal generation and meshing.
neper 3.5.2 neper/3.5 None application Applications Neper is a software package for polycrystal generation and meshing.
neptune 1.2.5 neptune/1.2 None application computational biology Neptune locates genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.
netcdf 4.2 netcdf/4.2 compiler/intel/18 library runtime support
netcdf 4.4 netcdf/4.4 compiler/gcc/9 library runtime support
netcdf 4.4.0 netcdf/4.4 compiler/intel/18 library runtime support
netcdf 4.5.0 netcdf/4.5 compiler/intel/20 compiler/gcc/9 compiler/gcc/10 compiler/intel/19 library runtime support
netcdf 4.7 netcdf/4.7 compiler/pgi/20 library runtime support
netcdf 4.7.0 netcdf/4.7 compiler/intel/19 compiler/intel/20 library runtime support
netcdf 4.7.4 netcdf/4.7 compiler/gcc/10 compiler/gcc/9 compiler/gcc/11 library runtime support
netica-c 5.04 netica-c/5.04 compiler/gcc/9 library mathematics
netlogo 6.2.2 netlogo/6.2 None application Simulation NetLogo is a multi-agent programmable modeling environment
netsurfp 1.0c netsurfp/1.0 None application computational biology NetSurfP predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.
nextdenovo 2.5.0 nextdenovo/2.5 None application Bioinformatics String graph-based de novo assembler for long reads (CLR, HiFi and ONT)
nextflow 20.04.1 nextflow/20.04 None application computational pipeline A DSL for data-driven computational pipelines http://nextflow.io
nextflow 21.04.0 nextflow/21.04 None application computational pipeline A DSL for data-driven computational pipelines http://nextflow.io
nextflow 21.10.6 nextflow/21.10 None application computational pipeline A DSL for data-driven computational pipelines http://nextflow.io
nextflow 22.10.6 nextflow/22.10 None application computational pipeline A DSL for data-driven computational pipelines http://nextflow.io
nextflow 23.04.1 nextflow/23.04 None application computational pipeline A DSL for data-driven computational pipelines http://nextflow.io
nextflow 23.10.1 nextflow/23.10 None application computational pipeline A DSL for data-driven computational pipelines http://nextflow.io
nextflow 24.04.3 nextflow/24.04 None application computational pipeline A DSL for data-driven computational pipelines http://nextflow.io
nextpolish 1.4.1 nextpolish/1.4 None application computational biology Fast and accurately polish the genome generated by long reads
nextstrain-cli 1.16.2 nextstrain-cli/1.16 None application computational biology Nextstrain: analysis and visualization of pathogen sequence data.
nextstrain-cli 3.0.3 nextstrain-cli/3.0 None application computational biology Nextstrain: analysis and visualization of pathogen sequence data.
nextstrain-cli 3.2.5 nextstrain-cli/3.2 None application computational biology Nextstrain: analysis and visualization of pathogen sequence data.
nextstrain-cli 4.2.0 nextstrain-cli/4.2 None application computational biology Nextstrain: analysis and visualization of pathogen sequence data.
ngmlr 0.2.7 ngmlr/0.2 None application computational biology ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore reads to a reference genome and optimized for structural variation detection
ninja 1.10.2 ninja/1.10 None application Utility A small build system with a focus on speed
ninja 1.12.1 ninja/1.12 None application Utility A small build system with a focus on speed
nlopt 2.7.1 nlopt/py39/2.7 None application algorithms nonlinear optimization library
nodejs 16.6.1 nodejs/16.6 None application system a platform for easily building fast, scalable network applications
nofold 1.0.1 nofold/1.0 None application computational biology NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment.
nomad 2.0.0 nomad/2.0 None application computational biology NOMAD is an unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence.
nquire 2018.04.05 nquire/2018.04.05 None application computational biology A statistical framework for ploidy estimation using NGS short-read data.
nucdiff 2.0.2 nucdiff/2.0 None application computational biology NucDiff locates and categorizes differences between two closely related nucleotide sequences.
nvim 0.9.5 nvim/0.9 None application utility Ambitious Vim-fork focused on extensibility and agility
nwchem 7.0.2 nwchem/7.0 compiler/gcc/9:openmpi/4.1 library runtime support
nwchem 7.2.2 nwchem/7.2 compiler/gcc/9:openmpi/4.1 library runtime support
oases 0.2.09 oases/0.2 None application computational biology Oases is de novo transcriptome assembler based on the Velvet genome assembler core.
octave 4.2 octave/4.2 None application engineering GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octave 6.1 octave/6.1 None application engineering GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octave 6.2 octave/6.2 None application engineering GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octave 7.2 octave/7.2 None application engineering GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octopus 13.0 octopus/13.0 compiler/intel/20:openmpi/4.1 application Applications
oma 2.4.1 oma/2.4 None application genomics OMA standalone is a standalone package that can infer orthologs using the OMA algorithm on custom genomes.
oncodriveclustl 1.1.3 oncodriveclustl/1.1 None application Biology OncodriveCLUSTL is a clustering method to identify cancer drivers
oncotator 1.9.9.0 oncotator/1.9 None application computational biology Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.
openbabel 3.1.1 openbabel/py37/3.1 None application chemistry A chemical toolbox designed to speak the many languages of chemical data
openbabel 3.1.1 openbabel/py38/3.1 None application chemistry A chemical toolbox designed to speak the many languages of chemical data
openblas 0.3.18 openblas/0.3 compiler/gcc/10 compiler/gcc/9 library tools Numerical library, contains blas/lapack
openbugs 3.2 openbugs/3.2 None application statistics BUGS is a software package for performing Bayesian inference Using Gibbs Sampling.
opencl 1.2 opencl/1.2 None library unknown This runtime software package adds OpenCL CPU device support on systems with Intel Core and Intel Xeon processors.
opencv 2.4.11 opencv/2.4 None library unknown Open Source Computer Vision Library
opencv 3.1.0 opencv/3.1 None library unknown Open Source Computer Vision Library
opencv 3.4.1 opencv/py27/3.4 None library unknown Open Source Computer Vision Library
opencv 3.4.1 opencv/py36/3.4 None library unknown Open Source Computer Vision Library
opencv 4.2.0 opencv/py27/4.2 None library unknown Open Source Computer Vision Library
opencv 4.2.0 opencv/py37/4.2 None library unknown Open Source Computer Vision Library
opencv 4.2.0 opencv/py38/4.2 None library unknown Open Source Computer Vision Library
opencv 4.5.5 opencv/4.5 compiler/gcc/11 library unknown Open Source Computer Vision Library
opencv 4.8.1 opencv/4.8 compiler/gcc/11 library unknown Open Source Computer Vision Library
openfoam 9 openfoam/9.0 compiler/gcc/11:openmpi/4.1 library runtime support
openjdk 10 openjdk/10 None application system OpenJDK (Java).
openjdk 11 openjdk/11 None application system OpenJDK (Java).
openjdk 12 openjdk/12 None application system OpenJDK (Java).
openjdk 13 openjdk/13 None application system OpenJDK (Java).
openjdk 14 openjdk/14 None application system OpenJDK (Java).
openjdk 15 openjdk/15 None application system OpenJDK (Java).
openjdk 16 openjdk/16 None application system OpenJDK (Java).
openjdk 17 openjdk/17 None application system OpenJDK (Java).
openjdk 18 openjdk/18 None application system OpenJDK (Java).
openjdk 19 openjdk/9 None application system OpenJDK (Java).
openjdk 19 openjdk/19 None application system OpenJDK (Java).
openjdk 20 openjdk/20 None application system OpenJDK (Java).
openjdk 21 openjdk/21 None application system OpenJDK (Java).
openjdk 22 openjdk/22 None application system OpenJDK (Java).
openjpeg 2.3.1 openjpeg/2.3 compiler/pgi/20 library runtime support
openjpeg 2.4 openjpeg/2.4 compiler/intel/20 compiler/pgi/20 compiler/gcc/10 compiler/intel/19 compiler/gcc/9 library runtime support
openmolcas 23.06 openmolcas/23.06 compiler/intel/20:openmpi/4.1 application quantum chemistry software package OpenMolcas is a quantum chemistry software package developed by scientists and intended to be used by scientists. It includes programs to apply many different electronic structure methods to chemical systems, but its key feature is the multiconfigurational approach, with methods like CASSCF and CASPT2.
openmpi 3.1 openmpi/3.1 compiler/nvhpc/21.9 library runtime support
openmpi 4.0 openmpi/4.0 compiler/intel/19 compiler/intel/18 compiler/gcc/10 compiler/gcc/9 compiler/intel/16 compiler/intel/20 compiler/gcc/11 compiler/pgi/20 library runtime support
openmpi 4.1 openmpi/4.1 compiler/intel/2021 compiler/intel/2024 compiler/gcc/10 compiler/pgi/20 compiler/intel/20 compiler/gcc/9 compiler/intel/18 compiler/gcc/11 compiler/intel/19 library runtime support
openmx 3.9 openmx/3.9 compiler/intel/20:openmpi/4.1 compiler/intel/20:openmpi/4.0 library runtime support
openslide 3.4.1 openslide/3.4 None application images OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
optuna 2.8.0 optuna/py37/2.8 None application Mathematics A hyperparameter optimization framework
optuna 2.8.0 optuna/py38/2.8 None application Mathematics A hyperparameter optimization framework
optuna 2.8.0 optuna/py39/2.8 None application Mathematics A hyperparameter optimization framework
orca 5.0.4 orca/5.0 compiler/gcc/11:openmpi/4.1 application quantum chemistry ORCA is an ab initio, DFT, and semi-empirical SCF-MO package.
orca 6.0.0 orca/6.0 compiler/gcc/11:openmpi/4.1 application quantum chemistry ORCA is an ab initio, DFT, and semi-empirical SCF-MO package.
orthofinder 1.1.8 orthofinder/1.1 None application computational biology OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthofinder 2.2.6 orthofinder/2.2 None application computational biology OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthofinder 2.5.5 orthofinder/2.5 None application computational biology OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthomcl 2.0.9 orthomcl/2.0 None application Biology Ortholog groups of protein sequences
p7zip 16.02 p7zip/16.02 None application System p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org ) for Unix.
paml 4.9 paml/4.9 None application Sequencing Phylogenetic Analysis by Maximum Likelihood (PAML)
pandaseq 2.11 pandaseq/2.11 None application bioinformatics PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
panphlan 1.3 panphlan/1.3 None application biology PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples.
panphlan 3.0 panphlan/3.0 None application biology PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples.
parallel-fastq-dump 0.6.5 parallel-fastq-dump/0.6 None application bioinformatics parallel fastq-dump wrapper
paraview 5.10.1 paraview/py37/5.10 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.10.1 paraview/py38/5.10 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.10.1 paraview/py39/5.10 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.11.1 paraview/py39/5.11 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.11.1 paraview/py310/5.11 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.11.1 paraview/py311/5.11 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.9.1 paraview/py37/5.9 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.9.1 paraview/py38/5.9 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview 5.9.1 paraview/py39/5.9 None application Utility ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview-headless 5.10 paraview-headless/5.10 compiler/gcc/11:openmpi/4.1 application Visualization
parmetis 4.0.3 parmetis/4.0 compiler/pgi/20:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/gcc/10:openmpi/4.0 compiler/intel/20:openmpi/4.0 compiler/gcc/9:openmpi/4.0 compiler/intel/20:openmpi/4.1 compiler/gcc/11:openmpi/4.1 library runtime support
parsinsert 1.04 parsinsert/1.04 None application computational biology ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm
pasa 2.3.3 pasa/2.3 None application computational biology PASA
pb-assembly 0.0.8 pb-assembly/0.0.8 None application Genomics Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin)
pbh5tools 0.8.0 pbh5tools/0.8 None application computational biology pbh5tools -- tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from "cmp.h5" and "bas.h5" files.
pblat 2.0 pblat/2.0 None application computational biology
peakranger 1.18 peakranger/1.18 None application computational biology PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data.
peakzilla 1.0 peakzilla/1.0 None application computational biology Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution.
pegasus-wms 5.0 pegasus-wms/5.0 None application workflow management system Pegasus Workflow Management System
pepr 1.1.18 pepr/1.1 None application computational biology Peak-calling and Prioritization pipeline for replicated ChIP-Seq data.
perl 5.22 perl/5.22 None application perl The Perl Programming Language
perl 5.26.2 perl/5.26 None application perl The Perl Programming Language
perl-mongodb 1.2.2 perl-mongodb/1.2 None application Utility This is the official Perl driver for MongoDB.
perl-pcap 3.5.2 perl-pcap/3.5 None application computational biology NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project
petsc 3.15 petsc/3.15 compiler/intel/20:openmpi/4.1 compiler/intel/20:openmpi/4.0 compiler/gcc/10:openmpi/4.0 library runtime support
phast 1.5 phast/1.5 None application bioinformatics PHAST is a freely available software package for comparative and evolutionary genomics.
phdf5 1.12.0 phdf5/1.12 compiler/intel/20:openmpi/4.1 compiler/gcc/10:openmpi/4.1 compiler/intel/19:openmpi/4.0 compiler/gcc/10:openmpi/4.0 compiler/gcc/9:openmpi/4.1 compiler/gcc/9:openmpi/4.0 compiler/intel/20:openmpi/4.0 compiler/intel/19:openmpi/4.1 library runtime support
phenix 1.18.2 phenix/1.18 compiler/gcc/9 library runtime support
phenix 1.19.2 phenix/1.19 compiler/gcc/9 library runtime support
phist 1.0.0 phist/1.0 None application computational biology Phage-Host Interaction Search Tool.
phobius 1.01 phobius/1.01 None application computational biology Phobius is a combined transmembrane topology and signal peptide predictor.
phono3py 1.18.1+3 phono3py/py27/1.18 None application Simulation A simulation package of phonon-phonon interaction related properties
phono3py 1.18.1+3 phono3py/py36/1.18 None application Simulation A simulation package of phonon-phonon interaction related properties
phono3py 1.18.1+3 phono3py/py37/1.18 None application Simulation A simulation package of phonon-phonon interaction related properties
phono3py 2.1.0 phono3py/py38/2.1 None application Simulation A simulation package of phonon-phonon interaction related properties
phono3py 2.1.0 phono3py/py39/2.1 None application Simulation A simulation package of phonon-phonon interaction related properties
phonopy 1.11.12 phonopy/1.11 None library runtime support
phonopy 2.11.0 phonopy/py37/2.11 None library runtime support
phonopy 2.11.0 phonopy/py39/2.11 None library runtime support
phylip 3.697 phylip/3.6 None library runtime support
phyloflash 3.4 phyloflash/3.4 None application Phylogeny phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
phylogenetics 0.5.0 phylogenetics/0.5 None application computational biology Python API for managing a phylogenetics projects.
phylophlan 1.0 phylophlan/1.0 None application computational biology Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
phylophlan 3.0.2 phylophlan/3.0 None application computational biology Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
phylosnp 1.0 phylosnp/1.0 None application computational biology PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data.
phyluce 1.6.8 phyluce/1.6 None application Genome reduction Software for UCE (and general) phylogenomics, and it is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.
phyml 3.3.20180621 phyml/3.3 None application Biology Phylogenetic estimation using (Maximum) Likelihood
picard 1.139 picard/1.1 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard 2.13 picard/2.13 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard 2.18.4 picard/2.18 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard 2.22.2 picard/2.22 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard 2.9.0 picard/2.9 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard 3.0.0 picard/3.0 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picrust 1.1.0 picrust/1.1 None application metagenomic The PICRUSt project aims to support prediction of the unobserved character states in a community of organisms from phylogenetic information about the organisms in that community.
picrust2 2.2.0_b picrust2/2.2 None application Pipeline PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
picrust2 2.4.1 picrust2/2.4 None application Pipeline PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
picrust2 2.5.2 picrust2/2.5 None application Pipeline PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
pilon 1.23 pilon/1.23 None application bioinformatics Pilon is an automated genome assembly improvement and variant detection tool.
pilon 1.24 pilon/1.24 None application bioinformatics Pilon is an automated genome assembly improvement and variant detection tool.
pindel 0.2.5b9 pindel/0.2 None application computational biology
pirs 2.0.2 pirs/2.0 None application computational biology
plasmidfinder 2.0.1 plasmidfinder/2.0 None application computational biology PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.
plasmidfinder 2.1 plasmidfinder/2.1 None application computational biology PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.
plink 1.90b4 plink/1.90 None application computational biology PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
plink2 2.0a1 plink2/2.0a1 None application computational biology This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others.
plinkseq 0.10 plinkseq/0.10 None application computational biology PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data.
plumed 2.8.0 plumed/2.8 compiler/gcc/10:openmpi/4.1 application molecular dynamics The community-developed PLUgin for MolEcular Dynamics.
plumed 2.8.1 plumed/2.8 compiler/gcc/11:openmpi/4.1 compiler/intel/20:openmpi/4.1 application molecular dynamics The community-developed PLUgin for MolEcular Dynamics.
plumed 2.9.0 plumed/2.9 compiler/intel/20:openmpi/4.1 compiler/gcc/11:openmpi/4.1 application molecular dynamics The community-developed PLUgin for MolEcular Dynamics.
pmlst 2.0.3 pmlst/2.0 None application Bioinformatics Plasmid Multi-Locus Sequence Typing
pomoxis 0.1.7 pomoxis/0.1 None application computational biology Assembly, consensensus, and analysis tools by ONT research
pomoxis 0.3.13 pomoxis/0.3 None application computational biology Assembly, consensensus, and analysis tools by ONT research
poplddecay 3.42 poplddecay/3.42 None application computational biology Fast and effective tool for linkage disequilibrium decay analysis.
popoolation2 1.201 popoolation2/1.201 None application Genomics PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.
poppunk 1.1.6 poppunk/1.1 None application computational biology PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
postgresql 15.2 postgresql/15.2 None application database PostgreSQL is a powerful, open source object-relational database system.
povray 3.7.0.8 povray/3.7 None application CGI The Persistence of Vision Raytracer.
pplacer 1.1 pplacer/1.1 None application computational biology Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
prank v.170427 prank/170427 None application bioinformatics PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.
primer3 2.3.7 primer3/2.3 None application computational biology Primer3 picks primers for PCR reactions
prinseq-lite 0.20.4 prinseq-lite/0.20 None application computational biology PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data
prodigal 2.6.3 prodigal/2.6 None application computational biology Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
prodigal 2.60 prodigal/2.60 None application computational biology Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
prohlatype 0.9.0 prohlatype/0.9 None application Computational Biology This project provides a set of tools to calculate the full posterior distribution of HLA types given read data.
proj 7.1.1 proj/7.1 compiler/intel/20 compiler/pgi/20 compiler/intel/19 compiler/gcc/9 compiler/gcc/10 library runtime support
prokka 1.12 prokka/1.12 None application bioinformatics Prokka is a software tool for the rapid annotation of prokaryotic genomes.
prokka 1.13.7 prokka/1.13 None application bioinformatics Prokka is a software tool for the rapid annotation of prokaryotic genomes.
prokka 1.14.6 prokka/1.14 None application bioinformatics Prokka is a software tool for the rapid annotation of prokaryotic genomes.
proteowizard 3_0_9992 proteowizard/3.0 None application computational biology ProteoWizard provides a modular and extensible set of open-source, cross-platform tools and libraries.
provean 1.1.5 provean/1.1 None application computational biology PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
psi4 1.9.1 psi4/py310/1.9 None application quantum chemistry Open-Source Quantum Chemistry - an electronic structure package in C++ driven by Python
psi4 1.9.1 psi4/py311/1.9 None application quantum chemistry Open-Source Quantum Chemistry - an electronic structure package in C++ driven by Python
pullseq 1.0 pullseq/1.0 None application computational biology pullseq - Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length.
purge_dups 1.2.6 purge_dups/1.2 None application Biology Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
pwtools 1.2.2 pwtools/py37/1.2 None application python pwtools is a Python package for pre- and postprocessing of atomistic calculations, mostly targeted to Quantum Espresso, CPMD, CP2K and LAMMPS.
pwtools 1.2.2 pwtools/py39/1.2 None application python pwtools is a Python package for pre- and postprocessing of atomistic calculations, mostly targeted to Quantum Espresso, CPMD, CP2K and LAMMPS.
pyani 0.2.11 pyani/py39/0.2 None application computational biology pyani provides a package and script for calculation of genome-scale average nucleotide identity.
pyclone 0.13 pyclone/0.13 None application computational biology PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples.
pydeface 2.0.2 pydeface/2.0 None application neuroimaging A tool to remove facial structure from MRI images.
pyfasta 0.5 pyfasta/0.5 None application computational biology Pyfasta - fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.
pygenometracks 2.0 pygenometracks/2.0 None application bioinformatics Standalone program and library to plot beautiful genome browser tracks.
pyicoteo 2.0.7 pyicoteo/2.0 None application Biology Analysis and manipulation of mapped reads coming from High Throughput Sequencing tool and library.
pymagic 0.1 pymagic/0.1 None application computational biology MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data.
pymatgen 2023.6.28 pymatgen/py39/2023.6.28 None application materials analysis Python Materials Genomics is an analysis code for materials science.
pymatgen 2023.6.28 pymatgen/py310/2023.6.28 None application materials analysis Python Materials Genomics is an analysis code for materials science.
pymatgen 2023.6.28 pymatgen/py311/2023.6.28 None application materials analysis Python Materials Genomics is an analysis code for materials science.
pymeteo 0.5 pymeteo/0.5 None application geoscience General meteorological routines, skew-T/log-p plotting and working with CM1 model data.
pymlst 0.0.2020.06.19 pymlst/2020.06.19 None application computational biology python Mlst Local Search Tool
pymol-open-source 2.4.0 pymol-open-source/py37/2.4 None application Molecular Dynamics A user-sponsored molecular visualization system
pymol-open-source 2.4.0 pymol-open-source/py38/2.4 None application Molecular Dynamics A user-sponsored molecular visualization system
pymol-open-source 2.4.0 pymol-open-source/py39/2.4 None application Molecular Dynamics A user-sponsored molecular visualization system
pymol-open-source 2.5.0 pymol-open-source/py39/2.5 None application Molecular Dynamics A user-sponsored molecular visualization system
pymol-open-source 2.5.0 pymol-open-source/py310/2.5 None application Molecular Dynamics A user-sponsored molecular visualization system
pymol-open-source 2.5.0 pymol-open-source/py311/2.5 None application Molecular Dynamics A user-sponsored molecular visualization system
pymongo 3.0.3 pymongo/3.0 None application Utility PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pymongo 3.3.0 pymongo/3.3 None application Utility PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pymongo 3.7.2 pymongo/3.7 None application Utility PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pysam 0.16.0.1 pysam/py37/0.16 None application bioinformatics Pysam is a python module for reading and manipulating Samfiles.
pysam 0.16.0.1 pysam/py38/0.16 None application bioinformatics Pysam is a python module for reading and manipulating Samfiles.
pyseer 1.2.0 pyseer/1.2 None application computational biology Sequence Elements Enrichment Analysis (SEER), python implementation
pyseer 1.3.4 pyseer/1.3 None application computational biology Sequence Elements Enrichment Analysis (SEER), python implementation
python 2.7 python/2.7 None application system
python 3.10 python/3.10 None application system
python 3.11 python/3.11 None application system
python 3.3 python/3.3 None application system
python 3.4 python/3.4 None application system
python 3.5 python/3.5 None application system
python 3.6 python/3.6 None application system
python 3.7 python/3.7 None application system
python 3.8 python/3.8 None application system
python 3.9 python/3.9 None application system
python-openstackclient 2.1.0 python-openstackclient/2.1 None application Utility Client for OpenStack services
python-openstackclient 6.0.0 python-openstackclient/6.0 None application Utility Client for OpenStack services
pytorch 0.4.1 pytorch/py27/0.4 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 0.4.1 pytorch/py35/0.4 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 0.4.1 pytorch/py36/0.4 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.10.0 pytorch/py38/1.10 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.10.0 pytorch/py39/1.10 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.12.1 pytorch/py38/1.12 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.12.1 pytorch/py39/1.12 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.13.0 pytorch/py39/1.13 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.13.0 pytorch/py310/1.13 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.2.0 pytorch/py27/1.2 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.2.0 pytorch/py36/1.2 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.2.0 pytorch/py37/1.2 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.5.1 pytorch/py37/1.5 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.6.0 pytorch/py37/1.6 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.7.1 pytorch/py37/1.7 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.7.1 pytorch/py38/1.7 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.8.0 pytorch/py37/1.8 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.8.0 pytorch/py38/1.8 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 1.8.0 pytorch/py39/1.8 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 2.0.0 pytorch/py310/2.0 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 2.0.0 pytorch/py311/2.0 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 2.3.1 pytorch/py39/2.3 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 2.3.1 pytorch/py311/2.3 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch-gpu 1.10.0 pytorch-gpu/py38/1.10 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 1.10.0 pytorch-gpu/py39/1.10 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 1.12.1 pytorch-gpu/py38/1.12 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 1.12.1 pytorch-gpu/py39/1.12 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 1.13.0 pytorch-gpu/py39/1.13 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 1.13.0 pytorch-gpu/py310/1.13 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 1.8.0 pytorch-gpu/py38/1.8 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 1.9.0 pytorch-gpu/py38/1.9 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 2.0.0 pytorch-gpu/py310/2.0 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 2.0.0 pytorch-gpu/py311/2.0 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 2.3.1 pytorch-gpu/py39/2.3 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu 2.3.1 pytorch-gpu/py311/2.3 None application deep learning Tensors and Dynamic neural networks in Python with strong GPU acceleration
qctool 1.4 qctool/1.4 None application computational biology QCTOOL is a command-line utility program for basic quality control of gwas datasets.
qgis 3.18.3 qgis/3.18 None application geographic information system A free and open source Geographic Information System (GIS).
qgis 3.30.2 qgis/3.30 None application geographic information system A free and open source Geographic Information System (GIS).
qgrs-cpp 2017.08.25 qgrs-cpp/2017.08.25 None application computational biology C++ implementation of QGRS mapping.
qiime 1.9.1 qiime/1.9 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime 2017.9 qiime/2.0 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2017.9 qiime2/2017.9 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2018.2 qiime2/2018.2 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2018.4 qiime2/2018.4 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2019.1 qiime2/2019.1 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2019.10 qiime2/2019.10 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2020.2.0 qiime2/2020.2 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2021.11.0 qiime2/2021.11 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2021.2 qiime2/2021.2 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2021.4.0 qiime2/2021.4 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2022.2.0 qiime2/2022.2 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2024.5.0 qiime2/2024.5 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qmpy 1.4.0 qmpy/py36/1.4 None application Physics A suite of computational materials science tools.
qmpy 1.4.0 qmpy/py37/1.4 None application Physics A suite of computational materials science tools.
qmpy 1.4.0 qmpy/py38/1.4 None application Physics A suite of computational materials science tools.
quake 0.3.5 quake/0.3 None application computational biology Quake is a package to correct substitution sequencing errors in experiments with deep coverage.
qualimap 2.3 qualimap/2.3 None application sequencing alignment Quality control of alignment sequencing data and its derivatives like feature counts
quasr 6.09 quasr/6.09 None application computational biology QUASR is lightweight pipeline for processing and analysis of high-throughput sequencing data.
quast 4.1 quast/4.1 None application computational biology QUAST evaluates genome assemblies by computing various metrics.
quast 4.4 quast/4.4 None application computational biology QUAST evaluates genome assemblies by computing various metrics.
quast 4.5 quast/4.5 None application computational biology QUAST evaluates genome assemblies by computing various metrics.
quast 5.0 quast/5.0 None application computational biology QUAST evaluates genome assemblies by computing various metrics.
r-asreml 4.1 r-asreml/r36/4.1 None application data analysis ASReml-R is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML) in the R environment.
r-asreml 4.1 r-asreml/r40/4.1 None application data analysis ASReml-R is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML) in the R environment.
r-asreml 4.2 r-asreml/r43/4.2 None application data analysis ASReml-R is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML) in the R environment.
r-fastbaps 1.0.1 r-fastbaps/r36/1.0 None application computational biology A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
r-fastbaps 1.0.6 r-fastbaps/r41/1.0 None application computational biology A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
r-genometricorr 1.1.17 r-genometricorr/r33/1.1 None application Genomics Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.
r-ggfortify 0.4.1 r-ggfortify/r33/0.4 None application r ggfortify is a package of unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis.
r-hmisc 4.6_0 r-hmisc/4.6 None application statistics Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.
r-inla 20.03.17 r-inla/r36/20.03.17 None application Mathematics Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations
r-keras 2.2.4.1 r-keras/r35/2.2 None application machine learning Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'.
r-markdown 0.8 r-markdown/r34/0.8 None application R Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.
r-matlib 0.9.2 r-matlib/r36/0.9 None application R A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods.
r-regresshaplo 1.0 r-regresshaplo/r34/1.0 None application biology This package reconstructs haplotypes from a BAM file using a penalized regression approach.
r-rhierbaps 1.1.2 r-rhierbaps/r35/1.1 None application computational biology rhierbaps is R implementation of hierBAPS.
r-rrblup 4.6.1 r-rrblup/r41/4.6 None application genomics Software for genomic prediction with the RR-BLUP mixed model.
r-scimpute 0.0.5 r-scimpute/0.0.5 None application biology scImpute is accurate and robust imputation of single-cell RNA sequencing data.
r-scimpute 0.0.6 r-scimpute/r34/0.0.6 None application biology scImpute is accurate and robust imputation of single-cell RNA sequencing data.
r-seqminer 6.0 r-seqminer/r34/6.0 None application biology SEQMINER is for sequencing variant annotation, data integration and query in R.
r-seurat 4.1.0 r-seurat/r41/4.1 None application computational biology A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
r-vcfr 1.5.0 r-vcfr/r34/1.5 None application biology A package to manipulate and visualize VCF data in R.
racon 1.5.0 racon/1.5 None application bioinformatics Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
rarefactionanalyzer 2018.09.06 rarefactionanalyzer/2018.09.06 None application computational biology Rarefaction analyzer is a simple program that can be used to perform rarefaction analysis.
raxml 8.2.12 raxml/8.2 None application Biology Phylogenetics - Randomized Axelerated Maximum Likelihood.
raxml-ng 1.0.3 raxml-ng/1.0 compiler/gcc/10:openmpi/4.1 application Genetics RAxML Next Generation: faster, easier-to-use and more flexible
raxml-ng 1.1.0 raxml-ng/1.1 compiler/gcc/10:openmpi/4.1 application Genetics RAxML Next Generation: faster, easier-to-use and more flexible
raxml-ng 1.2.0 raxml-ng/1.2 compiler/gcc/10:openmpi/4.1 application Genetics RAxML Next Generation: faster, easier-to-use and more flexible
ray 2.3.1 ray/2.3 None application computational biology Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.
rclone 1.44 rclone/1.44 None application Storage Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone 1.50.2 rclone/1.50 None application Storage Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone 1.51.0 rclone/1.51 None application Storage Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone 1.59.2 rclone/1.59 None application Storage Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone 1.64.2 rclone/1.64 None application Storage Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
read2tree 0.1.5 read2tree/py39/0.1 None application computational biology Building phylogenetic trees directly from sequencing reads
read2tree 0.1.5 read2tree/py310/0.1 None application computational biology Building phylogenetic trees directly from sequencing reads
readosm 1.1 readosm/1.1 compiler/gcc/9 unknown unknown
readosm 1.1.0a readosm/1.1 compiler/gcc/10 compiler/intel/19 compiler/intel/20 unknown unknown
reago 1.1 reago/1.1 None application bioinformatics Reconstructing 16S rRNA genes in metagenomic data.
red 2015.05.22 red/2015.05.22 None application Genomics Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
regtools 0.5.0 regtools/0.5 None application bioinformatics Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
relion 4.0.0 relion/4.0 compiler/intel/20:openmpi/4.1 application Physics
relion-gpu 4.0.0 relion-gpu/4.0 compiler/gcc/11:openmpi/4.1 application Physics
repeatmasker 4.0 repeatmasker/4.0 None application computational biology RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
repenrich 1.2 repenrich/1.2 None application computational biology RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
resfinder 4.1.11 resfinder/4.1 None application unknown ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.
resistomeanalyzer 2018.09.06 resistomeanalyzer/2018.09.06 None application computational biology Resistome Analyzer is a simple tool for analyzing the resistome of large metagenomic datasets.
retroseq 1.5 retroseq/1.5 None application bioinformatics RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.
revbayes 1.2.2 revbayes/1.2 compiler/gcc/11:openmpi/4.1 application Bioinformatics Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.
revtrans 1.4 revtrans/1.4 None application computational biology RevTrans - performs a reverse translation of a peptide alignment.
rgi 5.1.0 rgi/5.1 None application computational biology Resistance gene identifier.
rgi 5.2.1 rgi/5.2 None application computational biology Resistance gene identifier.
rgi 6.0.2 rgi/6.0 None application computational biology Resistance gene identifier.
rgt 0.11.4 rgt/0.11 None application computational biology Toolkit to perform regulatory genomics data analysis
ripgrep 13.0.0 ripgrep/13.0 None application Utility ripgrep recursively searches directories for a regex pattern
ripser 1.0.1 ripser/1.0 None application Bioinformatics Ripser: efficient computation of Vietoris–Rips persistence barcodes.
rmats 4.1.2 rmats/4.1 None application computational biology MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
rmats 4.3.0 rmats/4.3 None application computational biology MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
rnaclust 1.3 rnaclust/1.3 None application computational biology A tool for clustering of RNAs based on their secondary structures using LocARNA
rnahybrid 2.1.2 rnahybrid/2.1 None application computational biology RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA.
rnammer 1.2 rnammer/1.2 None application computational biology RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
rnaquast 1.5.1 rnaquast/1.5 None application Biology rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
rnasnp 1.2 rnasnp/1.2 None application computational biology Efficient detection of local RNA secondary structure changes induced by SNPs.
rnastructure 6.1 rnastructure/6.1 None application Bioinformatics RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.
roary 3.12.0 roary/3.12 None application computational biology Rapid large-scale prokaryote pan genome analysis
roary 3.13.0 roary/3.13 None application computational biology Rapid large-scale prokaryote pan genome analysis
rosetta 3.12 rosetta/3.12 compiler/gcc/9:openmpi/4.1 application computational biology The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
rosetta 3.13 rosetta/3.13 compiler/gcc/9:openmpi/4.1 application computational biology The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
rosettafold 1.0.0 rosettafold/1.0 None application bioinformatics RoseTTAFold - Accurate prediction of protein structures and interactions using a 3-track network.
rosettafold2na 0.2 rosettafold2na/0.2 None application computational biology RoseTTAFold2 protein/nucleic acid complex prediction.
rsem 1.2 rsem/1.2 None application computational biology RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
rsem 1.3 rsem/1.3 None application computational biology RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
rstudio 2023.12 rstudio/2023.12 None library runtime support RStudio is an integrated development environment (IDE) for R and Python.
rsync 3.1.3 rsync/3.1 None application System Tool for fast incremental file transfer
rsync 3.2.3 rsync/3.2 None application System Tool for fast incremental file transfer
ruby 2.1 ruby/2.1 None application system
rucs 1.0.2 rucs/1.0 None application computational biology RUCS is a bioinformatics tool developed to ease the task of designing new primers.
rust 1.41.0 rust/1.41 None application System Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. This package provides the compiler (rustc) and the documentation utilities rustdoc.
saga-gis 2.3 saga-gis/py27/2.3 None application Geoscience SAGA - System for Automated Geoscience Analysis.
saga-gis 8.3.1 saga-gis/py37/8.3 None application Geoscience SAGA - System for Automated Geoscience Analysis.
saga-gis 8.3.1 saga-gis/py38/8.3 None application Geoscience SAGA - System for Automated Geoscience Analysis.
saga-gis 8.3.1 saga-gis/py39/8.3 None application Geoscience SAGA - System for Automated Geoscience Analysis.
sage 6.3 sage/6.3 None application mathematics 'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.'
salmon 0.6.0 salmon/0.6 None application computational biology Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon 0.8.2 salmon/0.8 None application computational biology Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon 0.9.1 salmon/0.9 None application computational biology Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon 1.4.0 salmon/1.4 None application computational biology Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salsa2 2.3 salsa2/2.3 None application bioinformatics Salsa is a tool to scaffold long read assemblies with Hi-C.
sambamba 0.8.1 sambamba/0.8 None application Bioinformatics Tools for working with SAM/BAM data
samtools 0.1 samtools/0.1 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.15.1 samtools/1.15 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.17 samtools/1.17 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.19 samtools/1.19 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.20 samtools/1.20 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.3 samtools/1.3 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.5 samtools/1.5 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.6 samtools/1.6 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.9 samtools/1.9 None application computational biology Tools for dealing with SAM, BAM and CRAM files
sas 9.4 sas/9.4 None application Applications SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.
scaffold_builder 2.2 scaffold_builder/2.2 None application computational biology Scaffold_builder: Combining de novo and reference-guided assembly with Scaffold_builder.
scan-for-matches 1.0 scan-for-matches/1.0 None application computational biology scan_for_matches is a utility written in C for locating patterns in DNA or protein FASTA files.
schrodinger 2020.1 schrodinger/2020.1 None application Simulation Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
schrodinger 2020.4 schrodinger/2020.4 None application Simulation Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
schrodinger 2021.1 schrodinger/2021.1 None application Simulation Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
schrodinger 2022.1 schrodinger/2022.1 None application Simulation Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
scip 4.0.0 scip/4.0 None application constraint integer programming SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP).
scoary 1.6.16 scoary/py27/1.6 None application computational biology Microbial pan-GWAS using the output from Roary
scoary 1.6.16 scoary/py35/1.6 None application computational biology Microbial pan-GWAS using the output from Roary
scoary 1.6.16 scoary/py36/1.6 None application computational biology Microbial pan-GWAS using the output from Roary
scons 2.5 scons/2.5 None application utility SCons: A software construction tool.
scons 3.0 scons/3.0 None application utility SCons: A software construction tool.
scons 3.1.2 scons/py27/3.1 None application utility SCons: A software construction tool.
scons 3.1.2 scons/py38/3.1 None application utility SCons: A software construction tool.
scons 3.1.2 scons/py39/3.1 None application utility SCons: A software construction tool.
scons 4.2.0 scons/py37/4.2 None application utility SCons: A software construction tool.
scons 4.2.0 scons/py38/4.2 None application utility SCons: A software construction tool.
scons 4.2.0 scons/py39/4.2 None application utility SCons: A software construction tool.
scons 4.3.0 scons/py37/4.3 None application utility SCons: A software construction tool.
scons 4.3.0 scons/py38/4.3 None application utility SCons: A software construction tool.
scons 4.3.0 scons/py39/4.3 None application utility SCons: A software construction tool.
scythe 0.991 scythe/0.991 None application bioinformatics A 3'-end adapter contaminant trimmer.
seacr 1.3 seacr/1.3 None application computational biology SEACR is Sparse Enrichment Analysis for CUT&RUN
seedme 1.2 seedme/1.2 None application Utility Client program for SeedMe.org.
selecton 2.4 selecton/2.4 None application Bioinformatics Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.
sepp 1.0 sepp/1.0 None library runtime support
seqkit 0.10.1 seqkit/0.10 None application computational biology Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
seqkit 2.6.1 seqkit/2.6 None application computational biology Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
seqtk 1.2 seqtk/1.2 None application computational biology Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
seqyclean 1.10.07 seqyclean/1.10 None application Bioinformatics Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
settarg None settarg None unknown unknown The settarg module provides a way to connect the loaded modules with your build system by setting environment variables.
settarg settarg settarg/settarg None unknown unknown The settarg module provides a way to connect the loaded modules with your build system by setting environment variables.
sff2fastq 0.9.2 sff2fastq/0.9 None application computational biology The program sff2fastq extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.
shapeit 2.0 shapeit/2.0 None application computational biology SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shapeit 5.1.1 shapeit/5.1 None application computational biology SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shapelib 1.5.0 shapelib/1.5 compiler/intel/20 compiler/gcc/9 compiler/pgi/20 compiler/intel/19 compiler/gcc/10 library runtime support The Shapefile C Library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf).
shasta 0.11.1 shasta/0.11 None application Bioinformatics De novo assembly from Oxford Nanopore reads.
shasta 0.8.0 shasta/0.8 None application Bioinformatics De novo assembly from Oxford Nanopore reads.
shortbred 0.9.5 shortbred/0.9 None application bioinformatics ShortBRED is a system for profiling protein families of interest at very high specificity in shotgun metagenomic sequencing data.
shortstack 3.8.5 shortstack/3.8 None application Biology ShortStack: Comprehensive annotation and quantification of small RNA genes
shovill 1.0.9 shovill/1.0 None application computational biology Microbial assembly pipeline for Illumina paired-end reads
shrimp 2.2 shrimp/2.2 None application computational biology SHRiMP is a software package for aligning genomic reads against a target genome.
shtns 2.6.3 shtns/py36/2.6 None application high performance library SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
shtns 2.6.3 shtns/py310/2.6 None application high performance library SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
shtns 3.6 shtns/py36/3.6 None application high performance library SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
shtns 3.6 shtns/py310/3.6 None application high performance library SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
sicerpy 0.1.1 sicerpy/0.1 None application Biology Python wrapper around the popular ChIP-Seq peak caller SICER.
sickle 1.2 sickle/1.210 None application computational biology A windowed adaptive trimming tool for FASTQ files using quality
sickle 1.33 sickle/1.33 None application computational biology A windowed adaptive trimming tool for FASTQ files using quality
sift4g 2.0.0 sift4g/2.0 None application computational biology SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms.
signalp 4.1 signalp/4.1 None application Biology signalp predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes.
signalp 5.0b signalp/5.0b None application Biology signalp predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes.
simrna 3.20 simrna/3.20 None application computational biology SimRNA is a tool for simulations of RNA conformational dynamics
singularity 3.8 singularity/2.2 None application system Application containers enabling mobility of compute.
singularity 3.8 singularity/2.3 None application system Application containers enabling mobility of compute.
singularity 3.8 singularity/2.4 None application system Application containers enabling mobility of compute.
singularity 3.8 singularity/2.6 None application system Application containers enabling mobility of compute.
singularity 3.8 singularity/3.2 None application system Application containers enabling mobility of compute.
singularity 3.8 singularity/3.8 None application system Application containers enabling mobility of compute.
sistr_cmd 1.0.2 sistr_cmd/1.0 None application computational biology Salmonella In Silico Typing Resource command-line tool
sistr_cmd 1.1.1 sistr_cmd/1.1 None application computational biology Salmonella In Silico Typing Resource command-line tool
smetana 1.2.0 smetana/py36/1.2 None application genomics Species METabolic interaction ANAlysis (SMETANA) is a python-based command line tool to analyse microbial communities.
smrtlink 10.1.0.119588 smrtlink/10.1 None application Biology PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink 5.0.1 smrtlink/5.0 None application Biology PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink 5.1.0.26412 smrtlink/5.1 None application Biology PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink 7.0.1.66975 smrtlink/7.0 None application Biology PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
snakemake 5.18.0 snakemake/5.18 None application Utility A popular workflow management system aiming at full in-silico reproducibility.
snakemake 6.4.1 snakemake/6.4 None application Utility A popular workflow management system aiming at full in-silico reproducibility.
snap 2013-11-29 snap/2013-11-29 None application computational biology SNAP - (Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
sniffles 1.0.12 sniffles/1.0 None application computational biology Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)
sniffles 2.4 sniffles/2.4 None application computational biology Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)
snippy 4.3.6 snippy/4.3 None application computational biology Rapid bacterial SNP calling and core genome alignments
snippy 4.6.0 snippy/4.6 None application computational biology Rapid bacterial SNP calling and core genome alignments
snp-dists 0.6.3 snp-dists/0.6 None application computational biology Convert a FASTA alignment to SNP distance matrix
snp-dists 0.7.0 snp-dists/0.7 None application computational biology Convert a FASTA alignment to SNP distance matrix
snp-dists 0.8.2 snp-dists/0.8 None application computational biology Convert a FASTA alignment to SNP distance matrix
snp-pipeline 0.6 snp-pipeline/0.6 None application computational biology Script and functions for SNP matrix construction
snp-pipeline 0.7 snp-pipeline/0.7 None application computational biology Script and functions for SNP matrix construction
snp-pipeline 1.0 snp-pipeline/1.0 None application computational biology Script and functions for SNP matrix construction
snp-pipeline 2.0.2 snp-pipeline/2.0 None application computational biology Script and functions for SNP matrix construction
snp-sites 2.3.3 snp-sites/2.3 None application computational biology SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snp-sites 2.4.1 snp-sites/2.4 None application computational biology SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snp-sites 2.5.1 snp-sites/2.5 None application computational biology SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snpeff 4.3 snpeff/4.3 None application computational biology Genetic variant annotation and effect prediction toolbox.
snpeff 5.1 snpeff/5.1 None application computational biology Genetic variant annotation and effect prediction toolbox.
snpfinder 1.0.0 snpfinder/1.0 None application computational biology SNPFinder is a simple alignment-based haplotype variant caller that can be used with metagenomic sequence data.
snptest 2.5.2 snptest/2.5 None application computational biology SNPTEST is a program for the analysis of single SNP association in genome-wide studies.
soapdenovo-trans 1.04 soapdenovo-trans/1.04 None application computational biology SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
soapdenovo2 r240 soapdenovo2/r240 None application computational biology soapdenovo2 - novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes
sonnet 1.19 sonnet/py27/1.19 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 1.19 sonnet/py35/1.19 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 1.19 sonnet/py36/1.19 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 1.23 sonnet/py27/1.23 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 1.23 sonnet/py35/1.23 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 1.23 sonnet/py36/1.23 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 1.27 sonnet/py27/1.27 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 1.27 sonnet/py36/1.27 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 2.0.0 sonnet/py38/2.0 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet 2.0.0 sonnet/py39/2.0 None application machine learning Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet-gpu 1.19 sonnet-gpu/py27/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.19 sonnet-gpu/py35/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.19 sonnet-gpu/py36/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.23 sonnet-gpu/py27/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.23 sonnet-gpu/py35/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.23 sonnet-gpu/py36/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.27 sonnet-gpu/py27/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.27 sonnet-gpu/py36/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sortmerna 4.3.2 sortmerna/4.3.2 None application biological sequence analysis SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
spacy 2.2.3 spacy/py36/2.2 None application deep learning Industrial-strength Natural Language Processing
spacy 2.2.3 spacy/py37/2.2 None application deep learning Industrial-strength Natural Language Processing
spacy-gpu 2.2.4 spacy-gpu/py36/2.2 None application deep learning Industrial-strength Natural Language Processing
spacy-gpu 2.2.4 spacy-gpu/py37/2.2 None application deep learning Industrial-strength Natural Language Processing
spades 3.10.1 spades/3.10 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.11.1 spades/3.11 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.12.0 spades/3.12 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.13.0 spades/py27/3.13 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.13.0 spades/py35/3.13 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.13.0 spades/py36/3.13 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.14.0 spades/3.14 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.15.2 spades/3.15 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.8.1 spades/3.8 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
sparcc 0.1.0 sparcc/py27/0.1 None application computational biology SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).
sparta 18Jul2022 sparta/18Jul2022 compiler/gcc/11:openmpi/4.1 application Simulation Stochastic PArallel Rarefied-gas Time-accurate Analyzer.
spglib 2.0.2 spglib/2.0 compiler/intel/20 library runtime support
spider 2.0 spider/2.0 None application computational biology Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins.
spirit 2.1.1 spirit/py36/2.1 None application Physics Optimizations and Dynamics Framework for atomistic Spin systems
spirit 2.1.1 spirit/py37/2.1 None application Physics Optimizations and Dynamics Framework for atomistic Spin systems
spirit 2.1.1 spirit/py38/2.1 None application Physics Optimizations and Dynamics Framework for atomistic Spin systems
spirit-gpu 2.1.1 spirit-gpu/py36/2.1 None application Physics Optimizations and Dynamics Framework for atomistic Spin systems
spirit-gpu 2.1.1 spirit-gpu/py37/2.1 None application Physics Optimizations and Dynamics Framework for atomistic Spin systems
spirit-gpu 2.1.1 spirit-gpu/py38/2.1 None application Physics Optimizations and Dynamics Framework for atomistic Spin systems
spm 12 spm/12 compiler/gcc/11 application matlab toolbox Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.
spp 1.11 spp/1.11 None application computational biology ChIP-seq peak caller
spp 1.13 spp/1.13 None application computational biology ChIP-seq peak caller
spython 0.0.69 spython/0.0.69 None application singularity Command line python tool for working with singularity.
sqlite 3.33.0 sqlite/3.33 compiler/gcc/10 compiler/intel/20 compiler/pgi/20 compiler/intel/19 compiler/gcc/9 compiler/gcc/11 library runtime support
ssages 0.9.3 ssages/0.9gromacs compiler/gcc/9:openmpi/4.0 application molecular dynamics
ssages 0.9.3 ssages/0.9lammps compiler/gcc/9:openmpi/4.0 application molecular dynamics
ssake 4.0 ssake/4.0 None application genomics SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences.
stacks 2.4 stacks/2.4 None application computational biology Stacks is a software pipeline for building loci from RAD-seq
stamp 2.1.3 stamp/2.1 None application Taxonomy A graphical software package for analyzing taxonomic and functional profiles.
staphb-toolkit 1.3.6 staphb-toolkit/1.3 None application Bioinformatics The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the StaPH-B Docker Images to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
staphb-toolkit 20200304 staphb-toolkit/20200304 None application Bioinformatics The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the StaPH-B Docker Images to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
star 2.7.11b star/2.7 None application biology An RNA-seq read aligner.
star 2.7.9a star/2.7.9a None application biology An RNA-seq read aligner.
star-fusion 1.13.0 star-fusion/1.13 None application computational biology STAR-Fusion fusion variant caller.
star-fusion 1.9.0 star-fusion/1.9 None application computational biology STAR-Fusion fusion variant caller.
starccm 10.01.010 starccm/10.06 None library runtime support
starccm 9.01.011 starccm/9.06 None library runtime support
starship 1.20.1 starship/1.20 None application Cross-shell prompt The minimal, blazing-fast, and infinitely customizable prompt for any shell!
stereogene 2.20 stereogene/2.20 None application sequencing StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
strainest 1.2.4 strainest/1.2 None application Biology Abundance estimation of strains
strelka 2.9.10 strelka/2.9 None application computational biology Strelka calls somatic and germline small variants from mapped sequencing reads
stringmlst 0.6.3 stringmlst/0.6 None application computational biology Fast k-mer based tool for multi locus sequence typing (MLST) directly from genome sequencing reads
structure 2.3.4 structure/2.3 None application computational biology The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
subread 1.4.6p5 subread/1.4 None application computational biology The Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data.
subread 2.0.0 subread/2.0 None application computational biology The Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data.
subversion 1.10.8 subversion/1.10 None library tools Enterprise-class centralized version control for the masses
subversion 1.14.2 subversion/1.14 None library tools Enterprise-class centralized version control for the masses
suitesparse 5.10.1 suitesparse/5.10 compiler/gcc/10 library runtime support SuiteSparse: A Suite of Sparse matrix packages.
svn 1.10.8 svn/1.10 None library tools Enterprise-class centralized version control for the masses
svn 1.14.2 svn/1.14 None library tools Enterprise-class centralized version control for the masses
svsolver 2022.07.20 svsolver/2022.07.20 compiler/gcc/10:openmpi/4.1 application Biology The svSolver includes three executable programs: Presolver(svpre), Flowsolver(svsolver), Postsolver(svpost).
swan None swan None unknown unknown
sweepfinder2 1.0 sweepfinder2/1.0 None application Biology The BWA read mapper.
szip 2.1 szip/2.1 compiler/gcc/9 compiler/gcc/11 compiler/gcc/10 compiler/intel/18 library runtime support
szip 2.1.1 szip/2.1 compiler/intel/19 compiler/pgi/20 compiler/intel/20 library runtime support
t-coffee 13.39.0.d675aed t-coffee/13.39 None application computational biology A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
t-coffee 13.45.0.4846264 t-coffee/13.45 None application computational biology A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
tabix 0.2.6 tabix/0.2 None application computational biology A set of tools written in Perl and C++ for working with VCF files.
tagcleaner 0.16 tagcleaner/0.16 None application computational biology The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
targetfinder 1.7 targetfinder/1.7 None application computational biology Plant small RNA target prediction tool.
tassel 3.0 tassel/3.0 None application computational biology TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tassel 4.0 tassel/4.0 None application computational biology TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tassel 5.1 tassel/5.1 None application computational biology TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tassel 5.2.89 tassel/5.2 None application computational biology TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tax2tree 1.0 tax2tree/1.0 None application computational biology tax2tree - Tools for decorating taxonomy information on to a phylogenetic tree.
taxypro 1.0 taxypro/1.0 None application mixture modeling for taxonomic analysis of metagenomes
taxytoolbox 1.0 taxytoolbox/1.0 None application mixture modeling for taxonomic analysis of metagenomes
tciaclient 0.0.3 tciaclient/py38/0.0.3 None application TCIA TCIA (The Cancer Imaging Archive) Download Client for Python
tensorflow 0.12.1 tensorflow/py27/0.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 0.12.1 tensorflow/py35/0.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.0.0 tensorflow/py27/1.0 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.0.0 tensorflow/py35/1.0 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.11.0 tensorflow/py27/1.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.11.0 tensorflow/py36/1.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.12.0 tensorflow/py27/1.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.12.0 tensorflow/py36/1.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.14.0 tensorflow/py27/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.14.0 tensorflow/py36/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.14.0 tensorflow/py37/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.3.1 tensorflow/py27/1.3 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.3.1 tensorflow/py35/1.3 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.3.1 tensorflow/py36/1.3 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.4.0 tensorflow/py27/1.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.4.0 tensorflow/py35/1.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.4.0 tensorflow/py36/1.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.5.0 tensorflow/py27/1.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.5.0 tensorflow/py35/1.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.5.0 tensorflow/py36/1.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.7.0 tensorflow/py27/1.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.7.0 tensorflow/py35/1.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.7.0 tensorflow/py36/1.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.0.0 tensorflow/py36/2.0 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.0.0 tensorflow/py37/2.0 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.1.0 tensorflow/py36/2.1 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.1.0 tensorflow/py37/2.1 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.10.0 tensorflow/py38/2.10 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.10.0 tensorflow/py39/2.10 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.11.0 tensorflow/py38/2.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.11.0 tensorflow/py39/2.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.15.0 tensorflow/py310/2.15 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.15.0 tensorflow/py311/2.15 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.2.0 tensorflow/py36/2.2 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.2.0 tensorflow/py37/2.2 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.3.0 tensorflow/py37/2.3 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.3.0 tensorflow/py38/2.3 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.4.1 tensorflow/py37/2.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.4.1 tensorflow/py38/2.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.4.1 tensorflow/py39/2.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.5.0 tensorflow/py37/2.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.5.0 tensorflow/py38/2.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.5.0 tensorflow/py39/2.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.6.0 tensorflow/py38/2.6 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.6.0 tensorflow/py39/2.6 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.7.0 tensorflow/py38/2.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.7.0 tensorflow/py39/2.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.8.2 tensorflow/py38/2.8 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.8.2 tensorflow/py39/2.8 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.9.1 tensorflow/py38/2.9 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 2.9.1 tensorflow/py39/2.9 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.12.0 tensorflow-gpu/py27/1.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.12.0 tensorflow-gpu/py36/1.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.13.1 tensorflow-gpu/py27/1.13 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.13.1 tensorflow-gpu/py36/1.13 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.13.1 tensorflow-gpu/py37/1.13 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.14.0 tensorflow-gpu/py27/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.14.0 tensorflow-gpu/py36/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.14.0 tensorflow-gpu/py37/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.5.0 tensorflow-gpu/py27/1.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.5.0 tensorflow-gpu/py35/1.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.5.0 tensorflow-gpu/py36/1.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.7.0 tensorflow-gpu/py27/1.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.7.0 tensorflow-gpu/py35/1.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 1.7.0 tensorflow-gpu/py36/1.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.0.0 tensorflow-gpu/py36/2.0 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.0.0 tensorflow-gpu/py37/2.0 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.1.0 tensorflow-gpu/py36/2.1 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.1.0 tensorflow-gpu/py37/2.1 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.10.0 tensorflow-gpu/py38/2.10 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.10.0 tensorflow-gpu/py39/2.10 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.11.0 tensorflow-gpu/py38/2.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.11.0 tensorflow-gpu/py39/2.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.15.0 tensorflow-gpu/py310/2.15 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.15.0 tensorflow-gpu/py311/2.15 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.2.0 tensorflow-gpu/py36/2.2 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.2.0 tensorflow-gpu/py37/2.2 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.3.0 tensorflow-gpu/py38/2.3 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.4.1 tensorflow-gpu/py38/2.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.4.1 tensorflow-gpu/py39/2.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.5.0 tensorflow-gpu/py37/2.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.5.0 tensorflow-gpu/py38/2.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.5.0 tensorflow-gpu/py39/2.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.6.0 tensorflow-gpu/py38/2.6 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.6.0 tensorflow-gpu/py39/2.6 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.7.0 tensorflow-gpu/py38/2.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.7.0 tensorflow-gpu/py39/2.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.8.1 tensorflow-gpu/py38/2.8 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.8.1 tensorflow-gpu/py39/2.8 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.9.1 tensorflow-gpu/py38/2.9 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu 2.9.1 tensorflow-gpu/py39/2.9 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu py37/2.3 tensorflow-gpu/py37/2.3 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu py37/2.4 tensorflow-gpu/py37/2.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tf-comb 1.0.3 tf-comb/py38/1.0 None application Bioinformatics Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb 1.0.3 tf-comb/py39/1.0 None application Bioinformatics Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb 1.0.3 tf-comb/py310/1.0 None application Bioinformatics Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb 1.1 tf-comb/py38/1.1 None application Bioinformatics Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb 1.1 tf-comb/py39/1.1 None application Bioinformatics Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb 1.1 tf-comb/py310/1.1 None application Bioinformatics Transcription Factor Co-Occurrence using Market Basket analysis
theano 0.9.0 theano/py27/0.9 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 0.9.0 theano/py35/0.9 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 0.9.0 theano/py36/0.9 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 1.0.3 theano/py27/1.0 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 1.0.3 theano/py35/1.0 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 1.0.3 theano/py36/1.0 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
tmhmm 2.0c tmhmm/2.0c None None application computational biology TMHMM 2.0 predicts transmembrane helices in proteins.
tobias 0.13.3 tobias/py37/0.13 None application computational biology Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
topas-mc 3.9 topas-mc/3.9 None application Physics TOPAS: Tool for Particle Simulation
tophat 2.0.14 tophat/2.0 None application computational biology TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
tophat 2.1.1 tophat/2.1 None application computational biology TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
tpmcalculator 0.0.4 tpmcalculator/0.0.4 None application bioinformatics TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.
transcriptm 0.2 transcriptm/0.2 None application bioinformatics Metagenomics analyses.
transdecoder 2.0.1 transdecoder/2.0 None application computational biology TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
transdecoder 3.0.1 transdecoder/3.0 None application computational biology TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
transformers 4.31.0 transformers/py39/4.31 None application machine learning State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers 4.31.0 transformers/py310/4.31 None application machine learning State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers-gpu 4.31.0 transformers-gpu/py39/4.31 None application machine learning State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers-gpu 4.31.0 transformers-gpu/py310/4.31 None application machine learning State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transrate 0.1 transrate/0.1 None application life sciences transrate - Quality assessment and comparison of transcriptome assemblies
treemix 1.12 treemix/1.12 None application computational biology TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
treemix 1.13 treemix/1.13 None application computational biology TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
trf 4.07b trf/4.0 None application computational biology Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
triform2 0.0.5 triform2/0.0.5 None application computational biology Improved sensitivity, specificity and control of false discovery rates in ChIP-Seq peak finding.
trim_galore 0.4.5 trim_galore/0.4 None application computational biology Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control
trim_galore 0.6.5 trim_galore/0.6 None application computational biology Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control
trimmomatic 0.33 trimmomatic/0.33 None application computational biology A flexible read trimming tool for Illumina NGS data
trimmomatic 0.36 trimmomatic/0.36 None application computational biology A flexible read trimming tool for Illumina NGS data
trimmomatic 0.38 trimmomatic/0.38 None application computational biology A flexible read trimming tool for Illumina NGS data
trimmomatic 0.39 trimmomatic/0.39 None application computational biology A flexible read trimming tool for Illumina NGS data
trinity 2.11.0 trinity/2.11 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.12.0 trinity/2.12 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.13.2 trinity/2.13 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.15.1 trinity/2.15 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.4.0 trinity/2.4 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.6.6 trinity/2.6 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.8.4 trinity/2.8 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.9.1 trinity/2.9 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity r2013-11-10 trinity/r2013-11-10 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity r2014-04-13p1 trinity/r2014-04-13p1 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinotate 2.0.2 trinotate/2.0 None application computational biology Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
trinotate 3.2.1 trinotate/3.2 None application computational biology Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
trinotate r2013-11-10 trinotate/r2013-11-10 None application computational biology Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
trycycler 0.5.5 trycycler/0.5 None application bioinformatics A tool for generating consensus long-read assemblies for bacterial genomes
twincons 0.6.2.dev0 twincons/0.6 None application Biology This projects provides several packages for analysis of MSAs comprised of two sequence groups.
twobittofa 1.0 twobittofa/1.0 None unknown unknown This is a bioinformatics, freely downloadable command-line software (linux.x86_64) provided by the UCSC
ucsc-bedgraphtobigwig 455 ucsc-bedgraphtobigwig/455 None application computational biology Convert a bedGraph file to bigWig format.
ucsc-bigwigaverageoverbed 377 ucsc-bigwigaverageoverbed/377 None application computational biology Compute average score of big wig over each bed, which may have introns.
ucsc-fatotwobit 377 ucsc-fatotwobit/377 None application computational biology Convert DNA from fasta to 2bit format
ucsc-liftover 366 ucsc-liftover/366 None application computational biology The Batch Coordinate Conversion (liftOver) utility converts genome coordinates and genome annotation files between assemblies.
ucsc-twobittofa 357 ucsc-twobittofa/357 None application computational biology Convert all or part of .2bit file to fasta
ucsc-twobittofa 377 ucsc-twobittofa/377 None application computational biology Convert all or part of .2bit file to fasta
udunits2 2.2.26 udunits2/2.2 compiler/pgi/20 compiler/intel/20 library runtime support
ufcg 1.0.6 ufcg/1.0 None application computational biology UFCG pipeline provides methods for a genome-wide taxonomic profiling and annotation of your own biological sequences of Fungi.
ultraplex 1.2.9 ultraplex/1.2 None application computational biology fastq demultiplexer
umap-learn 0.2.4 umap-learn/py36/0.2 None application learning algorithm Uniform Manifold Approximation and Projection
umap-learn 0.3.10 umap-learn/py37/0.3 None application learning algorithm Uniform Manifold Approximation and Projection
umi_tools 1.0.1 umi_tools/1.0 None application Bioinformatics Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)
unicycler 0.4.8 unicycler/0.4 None application bioinformatics Hybrid assembly pipeline for bacterial genomes
unicycler 0.5.0 unicycler/0.5 None application bioinformatics Hybrid assembly pipeline for bacterial genomes
unikmer 0.18.7 unikmer/0.18 None application Biology unikmer: toolkit for nucleic acid k-mer analysis, including set operations on k-mers (sketch) optional with TaxIDs but without count information.
uropa 4.0.2 uropa/4.0 None application Biology UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for genomic region annotation from e.g. peak calling. It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction and strand into account. Furthermore, it allows filtering for GTF attribute values, e.g. protein_coding.
usearch 10.0.240 usearch/10.0 None application computational biology USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch 11.0.667 usearch/11.0 None application computational biology USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch 5.2 usearch/5.2 None application computational biology USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch 6.1 usearch/6.1 None application computational biology USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch 7.0 usearch/7.0 None application computational biology USEARCH is a unique sequence analysis tool with thousands of users world-wide.
varscan 2.3 varscan/2.3 None application computational biology Variant calling and somatic mutation/CNV detection for next-generation sequencing data
varscan 2.4.4 varscan/2.4 None application computational biology Variant calling and somatic mutation/CNV detection for next-generation sequencing data
vasp 5.4.4 vasp/5.4 compiler/intel/20:openmpi/4.1 library runtime support
vasp 6.2.1 vasp/6.2 compiler/intel/19:openmpi/4.1 library runtime support
vasp 6.2.1vtst vasp/6.2vtst compiler/intel/19:openmpi/4.1 library runtime support
vasp 6.3.1 vasp/6.3sol compiler/intel/20:openmpi/4.1 library runtime support
vasp 6.3.1 vasp/6.3vtst compiler/intel/20:openmpi/4.1 library runtime support
vasp 6.3.1 vasp/6.3 compiler/intel/20:openmpi/4.1 library runtime support
vasp 6.4.1 vasp/6.4sol compiler/intel/20:openmpi/4.1 library runtime support
vasp 6.4.1 vasp/6.4vtst compiler/intel/20:openmpi/4.1 library runtime support
vasp 6.4.3 vasp/6.4 compiler/intel/20:openmpi/4.1 library runtime support
vasp-acc 6.2.1 vasp-acc/6.2 compiler/intel/19 library runtime support
vasp-acc 6.3.1 vasp-acc/6.3 compiler/nvhpc/21.9:openmpi/3.1 compiler/intel/19 library runtime support
vasp-acc 6.4.1 vasp-acc/6.4 compiler/nvhpc/21.9:openmpi/3.1 library runtime support
vaspkit 1.5.1 vaspkit/1.5 None application Chemistry Perform high throughput analysis from data generated by VASP.
vcf-kit 0.1.6 vcf-kit/0.1 None application Utilities Assorted utilities for the variant call format
vcf2maf 1.6.18 vcf2maf/1.6 None application computational biology Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms
vcflib 1.0.2 vcflib/1.0 None application Utilities Command-line tools for manipulating VCF files
vcftools 0.1.16 vcftools/0.1 None application computational biology A set of tools written in Perl and C++ for working with VCF files.
vcontact2 0.9.19 vcontact2/0.9 None application Virology Viral Contig Automatic Clustering and Taxonomy
velvet 1.2.10 velvet/1.2 None application computational biology Velvet - Sequence assembler for very short reads
velvetoptimiser 2.2.6 velvetoptimiser/2.2 None application computational biology Automatically optimise three of Velvet's assembly parameters.
verifybamid2 2.0.1 verifybamid2/2.0 None application DNA sequencing A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
verkko 2.0 verkko/2.0 None application computational biology Assembler for hybrid combinations of long reads
vesta 3.5.8 vesta/3.5 None application visualization VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.
vflp 2020.04.19 vflp/2020.04.19 None application computational chemistry VFLP is VirtualFlow for Ligand Preparation
vftools 0.0.2020.05.17 vftools/2020.05.17 None application computational chemistry VFTools is a a loose collection of additional tools and scripts which can be useful when using VirtualFlow.
vfvs 2020.04.23 vfvs/2020.04.23 None application computational chemistry VFVS is VirtualFlow for Ligand Screenings
vfvs 2022.07.21 vfvs/2022.07.21 None application computational chemistry VFVS is VirtualFlow for Ligand Screenings
vgas 0.0.2020.07.22 vgas/2020.07.22 None application genomics VGAS (viral genome annotation system) is a system combing ab initio method and similarity-based method, which can perform the functions of virus gene finding and function annotating merely depending on the gene sequence itself.
vibrant 1.0.1 vibrant/1.0 None application computational biology Virus Identification By iteRative ANnoTation
vibrant 1.2.1 vibrant/1.2 None application computational biology Virus Identification By iteRative ANnoTation
viennarna 2.3.3 viennarna/2.3 None application computational biology The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
vigor4 0.0.2020.07.02 vigor4/2020.07.02 None application bioinformatics VIGOR4 (Viral Genome ORF Reader) is a Java application to predict protein sequences encoded in viral genomes.
vim 8.1.0960 vim/8.1 None application Utility Vim is a greatly improved version of the good old UNIX editor Vi
viral_consensus 0.0.5 viral_consensus/0.0.5 None application bioinformatics Fast viral consensus genome reconstruction
virema 0.6 virema/0.6 None application computational biology ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.
virhostmatcher 1.0.0 virhostmatcher/1.0 None application computational biology VirHostMatcher, matching hosts of viruses based on oligonucleotide frequency (ONF) comparison.
virhostmatcher-net 0.0.2021.08.29 virhostmatcher-net/2021.08.29 None application computational biology VirHostMatcher-Net: A network-based computational tool for predicting virus-host interactions.
virsorter 1.0.6 virsorter/1.0 None application unknown VirSorter2 -- A multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes
virsorter 2.1 virsorter/2.1 None application unknown VirSorter2 -- A multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes
visit 2.10.2 visit/2.10 None application utility VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
vistasoft 0fa6c4a vistasoft/0fa6c4a None application matlab toolbox VISTASOFT contains Matlab code to perform a variety of analysis on MRI data, including functional MRI and diffusion MRI.
vmd 1.9.3 vmd/1.9 None application molecular dynamics VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
vrhyme 1.1.0 vrhyme/1.1 None application bioinformatics vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
vs-code 1.90.2 vs-code/1.90 None application Development Visual Studio Code
vs-code-cli 1.90.2 vs-code-cli/1.90 None application Development Visual Studio Code
vsearch 2.10.0 vsearch/2.10 None application computational biology A versatile open source tool for metagenomics (USEARCH alternative)
vsearch 2.18.0 vsearch/2.18 None application computational biology A versatile open source tool for metagenomics (USEARCH alternative)
wannier90 3.1 wannier90/3.1 compiler/intel/20:openmpi/4.0 compiler/intel/19:openmpi/4.1 compiler/gcc/9:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/gcc/10:openmpi/4.1 compiler/gcc/10:openmpi/4.0 compiler/gcc/11:openmpi/4.1 compiler/intel/20:openmpi/4.1 library runtime support
wannierberri 0.11.1 wannierberri/py38/0.11 None application physics Advanced tool for Wannier interpolation and integration of k-space integrals
wannierberri 0.11.1 wannierberri/py39/0.11 None application physics Advanced tool for Wannier interpolation and integration of k-space integrals
wanniertools 2.7.0 wanniertools/2.7 compiler/intel/20:openmpi/4.1 application chemistry
weblogo 3.7.4 weblogo/3.7 None application Utility WebLogo3 : Sequence Logos Redrawn
wevote 1.8 wevote/1.8 None library runtime support
wgddetector 1.1 wgddetector/1.1 None application Biology WGDdetector: a pipeline for whole genome duplication (WGD) detecting with the genome or transcriptome annotations.
wgrib 1.8 wgrib/1.8 compiler/pgi/20 compiler/intel/20 application file processing WGRIB is a program to manipulate, inventory and decode GRIB files.
wgrib2 2.0.6 wgrib2/2.0 None application file processing wgrib2 is more like four drawers of kitchen utensils as well as the microwave and blender.
wtdbg 2.5 wtdbg/2.5 None application Bioinformatics Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
xcrysden 1.5.60 xcrysden/1.5 None application physics XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
xcrysden 1.6.2 xcrysden/1.6 None application physics XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
xpclr 1.1.2 xpclr/1.1 None application Bioinformatics Code to compute xp-clr values to detect selection as per Chen, Patterson & Reich 2010.
xzutils 5.2 xzutils/5.2 compiler/intel/19 compiler/intel/18 compiler/gcc/11 compiler/intel/20 None compiler/gcc/9 compiler/gcc/10 compiler/pgi/20 library runtime support
yambo 5.2.3 yambo/5.2 compiler/gcc/11:openmpi/4.1 application realistic materials Open-source many-body perturbation theory and time-dependent density functional theory
yaml-cpp 0.7 yaml-cpp/0.7 compiler/intel/20 compiler/gcc/10 library runtime support
zerone 1.0 zerone/1.0 None application computational biology Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.
zlib 1.2 zlib/1.2 compiler/gcc/9 None compiler/gcc/11 compiler/intel/19 compiler/pgi/20 compiler/intel/2021 compiler/intel/20 compiler/intel/18 compiler/gcc/10 library runtime support
zorro 2011.12.01 zorro/2011.12.01 None application bioinformatics ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple sequence alignment.