Available Software for Rhino
HCC provides some software packages via the Singularity container software. If you do not see a desired package in the module list below, please check the Using Singularity 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 2020-01-24T22:19:27CST
| Name | Version | Module Name | Prerequisites | Type | Domain | Description |
|---|---|---|---|---|---|---|
| R | 3.5.3 | R/3.5 | None | library | runtime support | R is a free software environment for statistical computing and graphics. |
| R | 3.6.1 | R/3.6 | None | library | runtime support | R is a free software environment for statistical computing and graphics. |
| SRAtoolkit | 2.10.0 | SRAtoolkit/2.10 | 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 |
| 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. |
| 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. |
| abricate | 0.8.13 | abricate/0.8 | None | application | Biology | Mass screening of contigs for antibiotic resistance genes |
| afni | 18.2.06 | afni/18.2 | None | application | MRI | AFNI is a suite of programs for looking at and analyzing 3D brain images. |
| 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. |
| 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. |
| 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 | 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 | |
| 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 | 3.3 | anaconda/3.3 | None | application | system | |
| anaconda | 3.4 | anaconda/3.4 | None | application | system | |
| anaconda | 4.3 | anaconda/4.3 | None | application | system | |
| anaconda | 4.6 | anaconda/4.6 | None | application | system | |
| 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 |
| anvio | 6.1 | anvio/6.1 | None | application | Omics | An interactive analysis and visualization platform for omics data |
| apkid | 1.0.0 | apkid/1.0 | None | application | Malware | APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android. |
| 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. |
| 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. |
| 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. |
| 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. |
| autoconf | 2.69 | autoconf/2.69 | None | application | Utilities | Extensible M4 macros that produce shell scripts to configure software source code packages. |
| 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. |
| automake | 1.16.1 | automake/1.16 | None | application | Utilities | Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. |
| awscli | 1.1.120 | awscli/1.11 | None | application | utility | The AWS CLI is an open source tool built on top of the AWS SDK for Python (Boto) that provides commands for interacting with AWS services. |
| 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. |
| 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. |
| 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 |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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 |
| 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. |
| binutils | 2.30 | binutils/2.30 | 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 |
| bioconductor | 3.4 | bioconductor/3.4 | 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-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 | 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 | 1.7.2 | 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 | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| biopython | 1.70 | biopython/py35/1.70 | None | application | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| biopython | 1.70 | biopython/py36/1.70 | None | application | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| biopython | 1.71 | biopython/py27/1.71 | None | application | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| biopython | 1.71 | biopython/py36/1.71 | None | application | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| biopython | 1.71 | biopython/py35/1.71 | None | application | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| biopython | 1.74 | biopython/py37/1.74 | None | application | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| biopython | 1.74 | biopython/py27/1.74 | None | application | biological computation | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. |
| 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. |
| boost | 1.70 | boost/1.70 | compiler/gcc/9.1 | application | System Environment/Base | Boost provides free peer-reviewed portable C++ source libraries. |
| 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 |
| 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/py27 | 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/py35 | 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/py36 | 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. |
| 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. |
| 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 |
| bx-python | 0.8.1 | bx-python/py27/0.8 | None | application | computational biology | Tools for manipulating biological data, particularly multiple sequence alignments |
| 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). |
| carnac-lr | 1.0.0 | carnac-lr/1.0 | None | application | computational biology | Clustering coefficient-based Acquisition of RNA Communities in Long Read |
| 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). |
| ccat | 3.0 | ccat/3.0 | None | application | computational biology | A software package for the analysis of ChIP-seq data with negative control. |
| cdo | 1.9.7.1 | cdo/1.9 | None | application | Utilities | CLI tools to manipulate and analyse Climate and NWP model Data |
| 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. |
| 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. |
| chemdata | 1.0 | chemdata/1.0 | None | application | computational chemistry | Static data resources for computational chemistry (docking, etc.). |
| circleator | 1.0.2 | circleator/1.0 | None | application | computational biology | Flexible circular visualization of genome-associated data with BioPerl and SVG. |
| clove | 0.17 | clove/0.17 | None | application | computational biology | CLOVE: Classification of genomic fusions into structural variation events. |
| 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 | 3.5.0 | 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 |
| 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. |
| compiler/gcc | 9.1 | compiler/gcc/9.1 | None | application | compiler | |
| compiler/intel | 19 | compiler/intel/19 | None | application | compiler | |
| compiler/pgi | 19 | compiler/pgi/19 | None | application | compiler | |
| connectome-workbench | 1.3.1 | 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 |
| cp2k | 6.1 | cp2k/6.1 | compiler/intel/19:openmpi/4.0 | library | runtime support | |
| cufflinks | 2.2.1 | cufflinks/2.2 | None | application | computational biology | Transcriptome assembly and differential expression analysis for RNA-Seq. |
| 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. |
| deap | 1.0 | deap/1.0 | None | application | computer science | DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. |
| deeptools | 2.5.4 | deeptools/2.5 | None | application | computational biology | |
| defiant | 2019.03.02 | defiant/2019.03.02 | None | application | computational biology | Differential methylation, Easy, Fast, Identification and ANnoTation. |
| delly | 0.8.1 | delly/0.8 | None | application | Biology | Structural variant discovery by integrated paired-end and split-read analysis |
| 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. |
| diamond | 0.9.25 | diamond/0.9 | None | application | Computational Biology | Accelerated BLAST compatible local sequence aligner |
| dmtcp | 2.6 | dmtcp/2.6 | compiler/intel/19:openmpi/4.0 compiler/gcc/9.1:openmpi/4.0 | application | Utility | |
| drep | 2.3.2 | drep/2.3 | None | application | Biology | De-replication of microbial genomes assembled from multiple samples |
| eigen | 3.3.3 | eigen/3.3 | None | application | C++ | C++ template library for linear algebra |
| emacs | 26.2 | emacs/26.2 | None | application | Utility | GNU Emacs is an extensible, customizable text editor. |
| 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. |
| 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. |
| 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. |
| eqtlbma | 1.3 | eqtlbma/1.3 | None | application | biology | Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging. |
| espresso | 6.4.1 | espresso/6.4 | compiler/intel/19:openmpi/4.0 | 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. |
| 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 |
| export2graphlan | 0.20 | export2graphlan/0.20 | None | application | bioinformatics | export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. |
| 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 |
| fastqc | 0.11.7 | fastqc/0.11 | 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 | 2.1.10 | fasttree/2.1 | None | application | computational biology | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. |
| feh | 3.3 | feh/3.3 | 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 |
| fftw3 | 3.3 | fftw3/3.3 | compiler/gcc/9.1:openmpi/4.0 compiler/intel/19:openmpi/4.0 | 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. |
| fqtrim | 0.9.7 | fqtrim/0.9 | None | application | computational biology | fqtrim: trimming & filtering of NGS reads. |
| freebayes | 1.2.0 | freebayes/1.2 | None | application | Biology | Bayesian haplotype-based polymorphism discovery and genotyping |
| freebayes | 1.3.1 | freebayes/1.3 | None | application | Biology | Bayesian haplotype-based polymorphism discovery and genotyping |
| 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 | 6.0.0 | freesurfer/6.0 | None | application | computational neuroimaging | An open source software suite for processing and analyzing (human) brain MRI images. |
| gamess | 20190930R2 | gamess/20190930R2 | compiler/intel/19:openmpi/4.0 | library | runtime support | |
| 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. |
| 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 | 4.1.2.0 | 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. |
| gaussian | 09 RevD | gaussian/09/RevD | None | application | Chemistry | |
| gaussian | 09 RevE | gaussian/09/RevE | None | application | Chemistry | |
| gaussian | 16 RevE | 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. |
| 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. |
| 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. |
| 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. |
| gensim | 3.8.0 | gensim/py37/3.8 | None | application | Machine learning | Topic Modelling for Humans |
| 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 |
| geoparse | 1.0.5 | geoparse/1.0 | None | application | Bioinformatics | Python library to access Gene Expression Omnibus Database (GEO) |
| gffcompare | 0.10.6 | gffcompare/0.10 | None | application | Annotation | GffCompare by Geo Pertea |
| 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. |
| 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 | 2.7.4 | git/2.7 | None | library | tools | distributed version control system |
| globus-cli | 1.10.1 | globus-cli/1.10 | None | application | tool | Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases. |
| globus-cli | 1.2.0 | globus-cli/1.2 | None | application | tool | Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases. |
| 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. |
| 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. |
| 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. |
| 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 |
| gradle | 3.3 | gradle/3.3 | None | application | Utility | Gradle is an open-source build automation tool focused on flexibility and performance. |
| gradle | 5.6 | gradle/5.6 | None | application | Utility | Gradle is an open-source build automation tool focused on flexibility and performance. |
| 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 | library | unknown | |
| gromacs | 2019.4 | gromacs/2019.4 | compiler/gcc/9.1:openmpi/4.0 | 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. |
| gtdbtk | 0.1.3 | gtdbtk/0.1 | 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. |
| 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. |
| 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. |
| halla | 0.8.17 | halla/0.8 | None | application | computational biology | HAllA: Hierarchically All-against-All Association Testing. |
| hdf5 | 1.10 | hdf5/1.10 | compiler/gcc/9.1 compiler/pgi/19 compiler/intel/19 | library | runtime support | |
| hipmcl | 1.6 | hipmcl/1.6 | compiler/gcc/9.1:openmpi/4.0 | application | network clustering | HipMCL is a high-performance parallel algorithm for large-scale network clustering. |
| 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 |
| 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 | 0.5.4p5 | 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 |
| 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. |
| 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 |
| 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. |
| 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. |
| intel-mkl | 19 | intel-mkl/19 | None | library | tools | Numerical library, contains blas/lapack |
| intel-mpi | 19 | intel-mpi/19 | compiler/intel/19 | library | runtime support | |
| 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. |
| 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 | 2.0 | jasper/2.0 | compiler/pgi/19 compiler/gcc/9.1 compiler/intel/19 | library | runtime support | |
| java | 1.6 | java/1.6 | None | application | system | Java JDK. |
| java | 1.7 | java/1.7 | None | application | system | Java JDK. |
| java | 1.8 | java/1.8 | None | application | system | Java JDK. |
| java | 11 | java/11 | None | application | system | Java JDK. |
| java | 12 | java/12 | None | application | system | Java JDK. |
| jq | 1.6 | jq/1.6 | None | application | Utility | A command-line JSON processor. |
| 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 |
| justorthologs | 0.0.20190308 | justorthologs/0.0.20190308 | None | application | Biology | JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. |
| 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 |
| 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. |
| 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 |
| 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 | 0.7.2 | 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. |
| 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 | 05Jun2019 | lammps/05Jun2019 | compiler/gcc/9.1:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/pgi/19:openmpi/4.0 | 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. |
| 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). |
| lmod | None | lmod | None | unknown | unknown | Lmod: An Environment Module System |
| logomaker | 0.8 | logomaker/py36/0.8 | None | application | Utility | Package for making Sequence Logos |
| logomaker | 0.8 | logomaker/py27/0.8 | None | application | Utility | Package for making Sequence Logos |
| 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. |
| 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. |
| macs2 | 2.1.1 | macs2/2.1 | None | application | computational biology | MACS -- Model-based Analysis of ChIP-Seq |
| mafft | 7.407 | mafft/7.407 | None | application | Bioinformatics | Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform |
| maker | 2.31.10 | maker/2.31 | None | application | computational biology | MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms. |
| 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. |
| 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 |
| 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. |
| mathematica | 10.0 | mathematica/10.0 | None | unknown | unknown | |
| mathematica | 10.4 | mathematica/10.4 | None | unknown | unknown | |
| mathematica | 11.0 | mathematica/11.0 | None | unknown | unknown | |
| mathematica | 11.3 | mathematica/11.3 | None | unknown | unknown | |
| mathematica | 9.0 | mathematica/9.0 | None | unknown | unknown | |
| 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 | |
| maxquant | 1.6.6.0 | maxquant/1.6 | None | application | biochemistry | MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. |
| 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 |
| 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 | 1.2.8 | 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 |
| megan | 6.12.3 | megan/6.12 | 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. |
| 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. |
| metasv | 0.5.4 | metasv/0.5 | None | application | computational biology | An accurate and integrative structural-variant caller for next generation sequencing. |
| 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 |
| methylpy | 1.4.1 | methylpy/py27/1.4 | 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 |
| methylpy | 1.4.1 | methylpy/py36/1.4 | None | application | bioinformatics | Bisulfite sequencing data processing and differential methylation analysis |
| micropita | 1.1.0 | micropita/1.1 | None | application | computational biology | microPITA is a computational tool enabling sample selection in two-stage (tiered) studies. |
| 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. |
| minimap2 | 2.16 | minimap2/2.16 | None | application | bioinformatics | A versatile pairwise aligner for genomic and spliced nucleotide sequences. |
| 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 |
| morgan | 3.4 | morgan/3.4 | None | application | computational biology | MORGAN is part of our software for Markov chain Monte Carlo in Genetic Analysis. |
| mosdepth | 0.2.4 | mosdepth/0.2 | 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. |
| 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. |
| 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 | 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 | 1.6 | 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. |
| 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 |
| 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. |
| nano | 2.9.8 | nano/2.9 | None | application | Utility | Nano's ANOther editor, an enhanced free Pico clone |
| ncbi-download | 0.2.6 | ncbi-download/0.2 | None | application | computational biology | Python scriopt for downloading bacterial and fungal genomes from NCBI. |
| 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. |
| neper | 3.3.0 | neper/3.3 | 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 | 4.7 | netcdf/4.7 | compiler/pgi/19 compiler/gcc/9.1 compiler/intel/19 | library | runtime support | |
| netcdf-c | 4.7 | netcdf-c/4.7 | compiler/intel/19 compiler/gcc/9.1 compiler/pgi/19 | library | runtime support | |
| netcdf-cxx4 | 4.3 | netcdf-cxx4/4.3 | compiler/pgi/19 compiler/intel/19 compiler/gcc/9.1 | library | runtime support | |
| netcdf-fortran | 4.4 | netcdf-fortran/4.4 | compiler/gcc/9.1 compiler/pgi/19 compiler/intel/19 | library | runtime support | |
| 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. |
| nucdiff | 2.0.2 | nucdiff/2.0 | None | application | computational biology | NucDiff locates and categorizes differences between two closely related nucleotide sequences. |
| nwchem | 6.8 | nwchem/6.8 | compiler/intel/19:openmpi/4.0 | 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. |
| 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. |
| opencv | 3.4.1 | opencv/py27/3.4 | None | library | unknown | OpenCV is a computer vision and machine learning software library. |
| opencv | 3.4.1 | opencv/py36/3.4 | None | library | unknown | OpenCV is a computer vision and machine learning software library. |
| openmpi | 4.0 | openmpi/4.0 | compiler/gcc/9.1 compiler/intel/19 compiler/pgi/19 | library | runtime support | |
| 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. |
| orthomcl | 2.0.9 | orthomcl/2.0 | None | application | Biology | Ortholog groups of protein sequences |
| 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. |
| parallel-fastq-dump | 0.6.5 | parallel-fastq-dump/0.6 | None | application | bioinformatics | parallel fastq-dump wrapper |
| pasa | 2.3.3 | pasa/2.3 | None | application | computational biology | PASA |
| 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. |
| 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 |
| 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/py27/1.18 | 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 |
| 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 | PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. |
| 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. |
| phyml | 3.3.20180621 | phyml/3.3 | None | application | Biology | Phylogenetic estimation using (Maximum) Likelihood |
| 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 | 2.9.0 | picard/2.9 | None | application | computational biology | A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. |
| picrust2 | 2.2.0_b | picrust2/2.2 | 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. |
| 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. |
| 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 | 2.5.3 | plumed/2.5 | compiler/gcc/9.1:openmpi/4.0 | application | molecular dynamics | The community-developed PLUgin for MolEcular Dynamics. |
| pomoxis | 0.1.7 | pomoxis/0.1 | None | application | computational biology | Pomoxis comprises APIs and command line tools for interacting and analysing Oxford Nanopore Technologies data in real time. |
| poppunk | 1.1.6 | poppunk/1.1 | None | application | computational biology | PopPUNK (POPulation Partitioning Using Nucleotide Kmers) |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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 | 3.4 | 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 | |
| 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/py36/0.4 | 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 | 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/py37/1.2 | 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. |
| qgrs-cpp | 2017.08.25 | qgrs-cpp/2017.08.25 | None | application | computational biology | C++ implementation of QGRS mapping. |
| 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. |
| quasr | 6.09 | quasr/6.09 | None | application | computational biology | QUASR is lightweight pipeline for processing and analysis of high-throughput sequencing data. |
| quast | 4.4 | 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/r34/4.1 | 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-fastbaps | 1.0.1 | r-fastbaps/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/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/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-keras | 2.2.4.1 | r-keras/2.2 | None | application | machine learning | Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. |
| r-markdown | 0.8 | r-markdown/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/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/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/1.1 | None | application | computational biology | rhierbaps is R implementation of hierBAPS. |
| r-scimpute | 0.0.6 | r-scimpute/0.0.6 | None | application | biology | scImpute is accurate and robust imputation of single-cell RNA sequencing data. |
| r-seqminer | 6.0 | r-seqminer/6.0 | None | application | biology | SEQMINER is for sequencing variant annotation, data integration and query in R. |
| r-vcfr | 1.5.0 | r-vcfr/1.5 | None | application | biology | A package to manipulate and visualize VCF data in R. |
| 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. |
| 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. |
| rclone | 1.50.2 | rclone/1.50 | None | application | Storage | Rclone - rsync for cloud storage. |
| 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. |
| repenrich | 1.2 | repenrich/1.2 | None | application | computational biology | RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data. |
| 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. |
| 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. |
| rgt | 0.11.4 | rgt/0.11 | None | application | computational biology | Toolkit to perform regulatory genomics data analysis |
| rhino | None | rhino | None | unknown | unknown | |
| ripser | 1.0.1 | ripser/1.0 | None | application | Bioinformatics | Ripser: efficient computation of VietorisRips persistence barcodes. |
| rnaclust | 1.3 | rnaclust/1.3 | None | application | computational biology | A tool for clustering of RNAs based on their secondary structures using LocARNA |
| 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 |
| 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. |
| 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. |
| 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. |
| 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. |
| 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/py36/1.6 | 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 |
| 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. |
| 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. |
| seqkit | 0.10.1 | seqkit/0.10 | 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 | |
| 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. |
| shortstack | 3.8.5 | shortstack/3.8 | None | application | Biology | ShortStack: Comprehensive annotation and quantification of small RNA genes |
| shovill | 1.0.4 | shovill/1.0 | None | application | computational biology | Microbial assembly pipeline for Illumina paired-end reads |
| siesta | 4.1.4 | siesta/4.1 | compiler/intel/19:openmpi/4.0 | library | runtime support | |
| 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. |
| singularity | 3.2 | singularity/2.3 | None | application | system | Application containers enabling mobility of compute. |
| singularity | 3.2 | singularity/2.2 | None | application | system | Application containers enabling mobility of compute. |
| singularity | 3.2 | singularity/3.2 | None | application | system | Application containers enabling mobility of compute. |
| singularity | 3.2 | singularity/2.6 | None | application | system | Application containers enabling mobility of compute. |
| singularity | 3.2 | singularity/2.4 | None | application | system | Application containers enabling mobility of compute. |
| sistr_cmd | 1.0.2 | sistr_cmd/1.0 | None | application | computational biology | |
| 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. |
| snippy | 4.3.6 | snippy/4.3 | None | application | computational biology | Rapid bacterial SNP calling and core genome alignments |
| 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. |
| snpeff | 4.3 | snpeff/4.3 | 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. |
| 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. |
| sonnet | 1.13 | sonnet/py35/1.13 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.13 | sonnet/py27/1.13 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.13 | sonnet/py36/1.13 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.19 | sonnet/py27/1.19 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.19 | sonnet/py35/1.19 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.19 | sonnet/py36/1.19 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.23 | sonnet/py36/1.23 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.23 | sonnet/py27/1.23 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.23 | sonnet/py35/1.23 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.27 | sonnet/py36/1.27 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| sonnet | 1.27 | sonnet/py27/1.27 | None | application | machine learning | Sonnet is a library built on top of TensorFlow for building complex neural networks. |
| 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/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/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/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 | 3.8.1 | 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). |
| spython | 0.0.69 | spython/0.0.69 | None | application | singularity | Command line python tool for working with singularity. |
| 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. |
| star | 2.7.1a | star/2.7 | None | application | biology | An RNA-seq read aligner. |
| stereogene | 2.20 | stereogene/2.20 | None | application | sequencing | StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data |
| strelka | 2.9.10 | strelka/2.9 | None | application | computational biology | Strelka calls somatic and germline small variants from mapped 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. |
| szip | 2.1 | szip/2.1 | compiler/pgi/19 compiler/gcc/9.1 compiler/intel/19 | library | runtime support | |
| targetfinder | 1.7 | targetfinder/1.7 | None | application | computational biology | Plant small RNA target prediction tool. |
| tassel | 5.2.40 | 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. |
| 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 | 1.11.0 | tensorflow/py27/1.11 | None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
| tensorflow | 1.12.0 | 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/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 | 1.14.0 | tensorflow/py27/1.14 | None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
| tensorflow | 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 | 2.0.0 | tensorflow/py36/2.0 | None | application | machine learning | TensorFlow is an open source software library for numerical computation using data flow graphs. |
| 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 | 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/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 | 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. |
| 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/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. |
| 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. |
| 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. |
| 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. |
| 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 | 0.6.4 | 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 | 0.36 | 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 |
| 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 |
| 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 | udunits2/2.2 | compiler/pgi/19 compiler/intel/19 compiler/gcc/9.1 | library | runtime support | |
| 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 |
| unicycler | 0.4.7 | unicycler/0.4 | None | application | bioinformatics | Hybrid assembly pipeline for bacterial genomes |
| usearch | 11.0.667 | usearch/11.0 | None | application | computational biology | USEARCH is a unique sequence analysis tool with thousands of users world-wide. |
| varscan | 2.4.3 | varscan/2.4 | None | application | computational biology | Variant calling and somatic mutation/CNV detection for next-generation sequencing data |
| vasp | 5.4.1 | vasp/5.4wan | compiler/intel/19:openmpi/4.0 | library | runtime support | |
| vasp | 5.4.4 | vasp/5.4 | compiler/intel/19:openmpi/4.0 | library | runtime support | |
| vcf-kit | 0.1.6 | vcf-kit/0.1 | None | application | Utilities | Assorted utilities for the variant call format |
| 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. |
| 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. |
| vibrant | 1.0.1 | vibrant/1.0 | 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. |
| vim | 8.1.0960 | vim/8.1 | None | application | Utility | Vim is a greatly improved version of the good old UNIX editor Vi |
| 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. |
| visit | 2.10.2 | visit/2.10 | None | application | utility | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. |
| vsearch | 2.10.0 | vsearch/2.10 | None | application | computational biology | A versatile open source tool for metagenomics (USEARCH alternative) |
| wannier | 1.2 | wannier/1.2 | compiler/intel/19 | library | runtime support | |
| weblogo | 3.7.4 | weblogo/3.7 | None | application | Utility | WebLogo3 : Sequence Logos Redrawn |
| 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. |
| 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/pgi/19 compiler/intel/19 compiler/gcc/9.1 | 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. |