last updated: Thursday, 15-Jun-2023 08:52:04 EDT
AdapterRemoval ============================================================================== Description: This program searches for and removes remnant adapter sequences from your read data. Versions: 2.3.1 License: GNU GENERAL PUBLIC LICENSE Categories: Bioinformatics ============================================================================== AFNI ============================================================================== Description: AFNI suite of MRI neuroimaging tools. Versions: 18.0.27; 22.2.07 License: https://afni.nimh.nih.gov/legal_info Categories: fMRI, DTI, MRI, neuroimaging, neuroscience ============================================================================== AMPL ============================================================================== Description: AMPL algebraic modeling language. Versions: 20220703 License: http://ampl.com/buy-ampl-terms-and-conditions/ Categories: Optimization, linear programming, algebraic modeling ============================================================================== Anaconda3 ============================================================================== Description: Python Data Science Distribution Versions: 2021.11; 2023.03 License: https://www.anaconda.com/eula-anaconda-individual-edition Categories: Python, Programming, Scripting, numpy, scipy, matplotlib, ipython, jupyter ============================================================================== angsd ============================================================================== Description: Angsd is a program for analysing NGS data. Versions: 0.935 License: N/A Categories: N/A ============================================================================== annotSV ============================================================================== Description: Annotation and Ranking of Human Structural Variations Versions: 2.2 License: GPLv2 Categories: Bioinformatics ============================================================================== annovar ============================================================================== Description: ANNOVAR is an efficient software tool to functionally annotate genetic variants detected from diverse genomes Versions: 9.2019 License: GPLv2 Categories: Bioinformatics ============================================================================== ANTs ============================================================================== Description: ANTs MRI image registration program Versions: 2.4.1 License: ANTs is Apache License 2.0 Categories: image processing, image registration, fMRI, neuroimaging ============================================================================== archivetar ============================================================================== Description: Parallel archive manipulation tool Versions: 0.15.4 License: https://github.com/brockpalen/archivetar/blob/master/LICENSE Categories: Utility ============================================================================== ARM Forge ============================================================================== Description: Parallel debugging and profiling tools, DDT and MAP. Versions: 21.1.3 License: Not available Categories: Programming, profiler, debugger, performance ============================================================================== aws-cli ============================================================================== Description: AWS command line interface Versions: False License: https://aws.amazon.com/terms/ Categories: Amazon, AWS, utility ============================================================================== bamtools ============================================================================== Description: C++ API & command-line toolkit for working with BAM data. Versions: 2.5.1; 2.5.2 License: N/A Categories: N/A ============================================================================== bbtools ============================================================================== Description: a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. Versions: 38.84 License: GPLv2 Categories: Bioinformatics ============================================================================== bcftools ============================================================================== Description: 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. Versions: 1.12 License: N/A Categories: N/A ============================================================================== bcl2fastq2 ============================================================================== Description: The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files. Versions: 2.20.0.422 License: N/A Categories: N/A ============================================================================== beast1 ============================================================================== Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. Versions: 1.10.4 License: N/A Categories: N/A ============================================================================== bedtools2 ============================================================================== Description: Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. Versions: 2.25.0; 2.30.0 License: N/A Categories: N/A ============================================================================== blast-plus ============================================================================== Description: Basic Local Alignment Search Tool. Versions: 2.12.0 License: N/A Categories: N/A ============================================================================== blat ============================================================================== Description: BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm. Versions: 35 License: N/A Categories: N/A ============================================================================== Boost ============================================================================== Description: Boost C++ library collection. Versions: 1.78.0 License: http://www.boost.org/users/license.html Categories: Programming, C++, library ============================================================================== bowtie2 ============================================================================== Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences Versions: 2.4.1; 2.4.2 License: N/A Categories: N/A ============================================================================== bwa ============================================================================== Description: Burrow-Wheeler Aligner for pairwise alignment between DNA sequences. Versions: 0.7.15; 0.7.17 License: N/A Categories: N/A ============================================================================== canu ============================================================================== Description: A single molecule sequence assembler for genomes large and small. Versions: 2.2 License: N/A Categories: N/A ============================================================================== cap3 ============================================================================== Description: CAP3 is DNA Sequence Assembly Program Versions: 2015-02-11 License: N/A Categories: N/A ============================================================================== clustal-omega ============================================================================== Description: Clustal Omega: the last alignment program you'll ever need. Versions: 1.2.4 License: N/A Categories: N/A ============================================================================== CMake ============================================================================== Description: CMake cross-platform make system. Versions: 3.22.2; 3.26.3 License: https://cmake.org/licensing/ Categories: Utility, programming, compiler ============================================================================== cuda ============================================================================== Description: CUDA compilers and libraries. Versions: 10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0; 12.1.1 License: http://docs.nvidia.com/cuda/eula/index.html Categories: CUDA, gpu, library, programming ============================================================================== cudnn ============================================================================== Description: cuDNN libraries. Versions: 10.2-v8.3.1; 11.2-v8.1.1; 11.3-v8.2.1; 11.5-v8.3.1; 11.6-v8.4.1; 11.7-v8.7.0; 11.8-v8.7.0; 12.1-v8.9.0 License: https://docs.nvidia.com/deeplearning/cudnn/sla Categories: CUDA, gpu, library, programming, cuDNN, deep learning, neural network ============================================================================== cufflinks ============================================================================== Description: Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA- Seq samples. Versions: 2.2.1 License: N/A Categories: N/A ============================================================================== CUPTI ============================================================================== Description: CUDA Profiler Tools Interface Versions: 10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0; 12.1.1 License: http://docs.nvidia.com/cuda/eula Categories: CUDA, gpu, library, programming, Profiler ============================================================================== DeepLabCut ============================================================================== Description: DeepLabCut™ is an efficient method for 2D and 3D markerless pose estimation Versions: 2.1.10.4 License: GPLv3 Categories: Bioinformatics ============================================================================== delly2 ============================================================================== Description: Delly2 is an integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single- nucleotide resolution in short-read massively parallel sequencing data.. Versions: 0.9.1 License: N/A Categories: N/A ============================================================================== Eigen ============================================================================== Description: Linear algebra template library Versions: 3.4.0 License: https://eigen.tuxfamily.org/index.php Categories: Linear algebra, numerical, development, library ============================================================================== epacts ============================================================================== Description: EPACTS - Efficient and Parallelizable Association Container Toolbox Versions: 3.4.2 License: GNU GPL3 Categories: Bioinformatics ============================================================================== fastcn ============================================================================== Description: A pipeline for the fast estimation of copy-number based on read depth using the multi-mapper mrsFAST. Versions: 1.0 License: GPL Categories: Bioinformatics ============================================================================== fastqc ============================================================================== Description: A quality control tool for high throughput sequence data. Versions: 0.11.5; 0.11.9 License: N/A Categories: N/A ============================================================================== FFMPEG ============================================================================== Description: FFMPEG is a complete, cross-platform solution to record, convert and stream audio and video. Versions: 4.4.2 License: https://ffmpeg.org/legal.html Categories: audio, video, codec, transcoder ============================================================================== fftw ============================================================================== Description: Libraries for computation of discrete Fourier transform. Versions: 3.3.10 License: http://www.fftw.org/fftw3_doc/License-and-Copyright.html Categories: Library, Development, Core ============================================================================== figtree ============================================================================== Description: FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST. Versions: 1.4.4 License: N/A Categories: N/A ============================================================================== fiji ============================================================================== Description: fiji is just ImageJ Versions: 1.5.3 License: GPLv2 Categories: Bioinformatics ============================================================================== FreeSurfer ============================================================================== Description: FreeSurfer MRI processing and analysis software. Versions: 7.2.0 License: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLi cense Categories: MRI, neuroimaging, neuroscience ============================================================================== FSL ============================================================================== Description: FSL suite of MRI neuroimaging tools. Versions: 6.0.5.2 License: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence Categories: fMRI, DTI, neuroimaging, neuroscience ============================================================================== gatk ============================================================================== Description: Toolkit for variant discovery and genotyping Versions: 3.7; 4.2.2.0 License: Broad Institute Software License Agreement Categories: Bioinformatics ============================================================================== gcc ============================================================================== Description: GNU compiler suite Versions: 10.3.0 License: GPL Categories: Compiler, programming, development ============================================================================== GDAL ============================================================================== Description: GDAL is a translator library for raster and vector geospatial data formats. Versions: 3.5.1 License: https://gdal.org/license.html Categories: GIS, geospatial, raster, vector, graphics ============================================================================== GEOS ============================================================================== Description: OpenGIS Simple Features for SQL spatial predicate functions and spatial operators. Versions: 3.10.2 License: GNU LGPL v2.1 Categories: GIS, Geometry, OSGeo ============================================================================== git ============================================================================== Description: Git version control software Versions: 2.39.1 License: GPL version 2 Categories: Utility, development, version control ============================================================================== git-annex ============================================================================== Description: Manage large files with git, without storing the file contents in git Versions: 10.20220928 License: AGPL version 3.0 Categories: Utility, development, version control, file management ============================================================================== Go ============================================================================== Description: The Go programming language is an open source project to make programmers more productive. Versions: 1.18 License: https://go.dev/LICENSE?m=text Categories: Go, Programming, golang ============================================================================== groff ============================================================================== Description: GNU roff Versions: 1.22.4 License: GNU Categories: Bioinformatics ============================================================================== GSL ============================================================================== Description: GNU scientific libraries Versions: 2.7 License: GPL Categories: Programming, library, mathematics ============================================================================== Gurobi ============================================================================== Description: Gurobi optimization problem solver. Versions: 9.5.1 License: http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf Categories: Optimization, linear programming ============================================================================== HDF5 ============================================================================== Description: HDF5 data libraries and utilities. Versions: 1.10.8; 1.8.22 License: https://www.hdfgroup.org/products/licenses.html Categories: Utility, programming, library ============================================================================== Hello ============================================================================== Description: Hello world example of writing a module. Versions: 1.0 License: N/A Categories: N/A ============================================================================== hisat2 ============================================================================== Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). Versions: 2.2.0 License: N/A Categories: N/A ============================================================================== homer ============================================================================== Description: Software for motif discovery and next generation sequencing analysis Versions: 4.11.1 License: N/A Categories: N/A ============================================================================== HPC compilers ============================================================================== Description: Compiler suite. Versions: 22.3 License: https://docs.nvidia.com/hpc-sdk/eula/hpc-sdk-ea-eula.pdf Categories: Compiler, development, debugger, profiler ============================================================================== htslib ============================================================================== Description: C library for high-throughput sequencing data formats. Versions: 1.12; 1.13; 1.9 License: N/A Categories: N/A ============================================================================== humann ============================================================================== Description: HMP Unified Metabolic Analysis Network Versions: 3.0.1 License: GPLv2 Categories: Bioinformatics ============================================================================== igv ============================================================================== Description: The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. Versions: 2.8.9 License: N/A Categories: N/A ============================================================================== Image libraries ============================================================================== Description: Image libraries Versions: 220318.1; 220318 License: more than one Categories: libraries, programming, jpeg, gif, png, jbigkit, tiff, libwebp, lcms2, jasper, ImageMagick ============================================================================== imagemagick ============================================================================== Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images. Versions: 7.1.0-33 License: N/A Categories: N/A ============================================================================== impi ============================================================================== Description: Intel MPI runtime Versions: 2021.5.1; 2018.4.274 License: GPL Categories: MPI, MPICH, programming ============================================================================== impute2 ============================================================================== Description: IMPUTE2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009. Versions: 2.3.2 License: N/A Categories: N/A ============================================================================== Intel ============================================================================== Description: Intel compiler suite. Versions: 18.0.5; 2022.1.2 License: None provided Categories: Library, Development, Core ============================================================================== ITK ============================================================================== Description: ITK is an open-source system for medical image processing. Versions: 5.2.1 License: https://software.intel.com/en-us/license/intel-simplified- software-license Categories: Library, development, image processing, MRI, NIfTI ============================================================================== itk ============================================================================== Description: The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. Versions: 5.2.1 License: N/A Categories: N/A ============================================================================== iVar ============================================================================== Description: iVar is a computational package that contains functions for viral amplicon-based sequencing Versions: 1.2.1 License: GPLv2 Categories: Bioinformatics ============================================================================== JAGS ============================================================================== Description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models. Versions: 4.3.0 License: GNU GPL v2 Categories: Bayesian, Markov, MCMC ============================================================================== joe ============================================================================== Description: JOE editor. Versions: 4.6 License: https://joe-editor.sourceforge.io/ Categories: Editor, development, utility ============================================================================== Julia ============================================================================== Description: Julia is a high-level, high-performance dynamic language for technical computing. The main homepage for Julia can be found at julialang.org. Versions: 1.7.2 License: MIT Licenses Categories: Programming ============================================================================== kallisto ============================================================================== Description: kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. Versions: 0.46.0 License: BSD Simplified 2-Clause Categories: Bioinformatics ============================================================================== LAPACK ============================================================================== Description: LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least- squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. Versions: 3.10.1 License: http://www.netlib.org/lapack/LICENSE.txt Categories: Libraries ============================================================================== Launcher ============================================================================== Description: A framework for running large collections of serial or multi- threaded applications Versions: 3.7 License: GPLv2 Categories: Core ============================================================================== Mathematica ============================================================================== Description: Mathematical and technical computing package. Versions: 12.3.1 License: http://www.wolfram.com/legal/agreements/wolfram- mathematica.html Categories: Mathematics, symbolic algebra ============================================================================== Matlab ============================================================================== Description: Matlab programming environment. Versions: R2021b; R2022b License: N/A Categories: Mathematics, programming, simulation ============================================================================== Matplotlib ============================================================================== Description: Visualization with Python. Versions: 3.5.3 License: https://github.com/matplotlib/matplotlib/tree/main/LICENSE Categories: Programming, python, visualization, graph, image ============================================================================== megahit ============================================================================== Description: MEGAHIT is an ultra-fast and memory-efficient NGS assemble Versions: 1.2.9 License: GPLv3 Categories: Bioinformatics ============================================================================== metaphlan3 ============================================================================== Description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data Versions: 3.0 License: GPLv2 Categories: Bioinformatics ============================================================================== minimap2 ============================================================================== Description: Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Mappy provides a convenient interface to minimap2. Versions: 2.14 License: N/A Categories: N/A ============================================================================== MKL ============================================================================== Description: Intel optimized BLAS/LAPACK libraries, also including FFT and other mathematical and statistical routines. Versions: 2018.0.4 License: https://software.intel.com/en-us/license/intel-simplified- software-license Categories: Library, Development, Core, BLAS, LAPACK ============================================================================== mothur ============================================================================== Description: This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Versions: 1.46.1 License: N/A Categories: N/A ============================================================================== MPI for Python (mpi4py) ============================================================================== Description: Numerical libraries for use within Python. Versions: 3.1.3 License: https://github.com/mpi4py/mpi4py/blob/master/LICENSE.rst Categories: Programming, python, MPI, mpi4py ============================================================================== MPIFileUtils ============================================================================== Description: Parallel file manipulation utilities. Versions: 0.10.2-arcts License: https://github.com/brockpalen/mpifileutils/blob/master/LICENSE Categories: Utility ============================================================================== MRtrix ============================================================================== Description: MRtrix provides a set of tools to perform various advanced diffusion MRI analyses. Versions: 3.0.4; 3.0.3-dfd3360 License: Mozilla Public License, http://mozilla.org/MPL/2.0/ Categories: fMRI, diffusion-weighted MRI, tractography, neuroimaging ============================================================================== ncftp ============================================================================== Description: NcFTP Client is a set of application programs implementing the File Transfer Protocol. Versions: 3.2.6 License: N/A Categories: N/A ============================================================================== NetCDF ============================================================================== Description: Libraries for creating and manipulating NetCDF files. Versions: 4.8.1 License: https://www.ucar.edu/terms-of-use Categories: Library, Development, Core ============================================================================== NetCDF Fortran ============================================================================== Description: Libraries for creating and manipulating NetCDF files using Fortran. Versions: 4.5.3 License: https://www.ucar.edu/terms-of-use Categories: Library, Development, Core ============================================================================== NetCDF-CXX ============================================================================== Description: C++ API to the NetCDF-C libraries. Versions: 4.3.1 License: https://www.ucar.edu/terms-of-use Categories: Library, Development, Core ============================================================================== new_fugue ============================================================================== Description: a program that calculates linkage disequilibrium measures from genotype files. Versions: 2010-05-25 License: GPLv2 Categories: Bioinformatics ============================================================================== NumPy ============================================================================== Description: Numerical libraries for use within Python. Versions: 1.22.3 License: https://github.com/numpy/numpy Categories: Programming, numerical library, BLAS, LAPACK, python ============================================================================== openblas ============================================================================== Description: BLAS provides standard interfaces for linear algebra, including vector-vector operations, matrix-vector operations, and matrix-matrix operations. Versions: 0.3.19 License: https://opensource.org/licenses/BSD-3-Clause Categories: Programming, C++, library ============================================================================== OpenJDK ============================================================================== Description: OpenJDK is a free and open-source implementation of the Java Platform. Versions: 18.0.1.1 License: GPLv2 with linking exception Categories: Java, programming ============================================================================== OpenMPI ============================================================================== Description: OpenMPI implementation of the MPI protocol Versions: 4.1.3; 4.1.4; 4.1.2 License: https://www.open-mpi.org/community/license.php Categories: Utility, Development, Core ============================================================================== openslide ============================================================================== Description: OpenSlide reads whole slide image files. Versions: 3.4.1 License: N/A Categories: N/A ============================================================================== Pandas ============================================================================== Description: Data analysis and manipulation. Versions: 1.4.2 License: https://github.com/pandas-dev/pandas Categories: Programming, statistics, data analysis, data management, python ============================================================================== Pandoc ============================================================================== Description: A universal document converter. Versions: 2.17.1.1 License: http://www.gnu.org/copyleft/gpl.html Categories: Utility, document converter, markup ============================================================================== Parabricks ============================================================================== Description: Parabricks is a software suite for performing secondary analysis of next generation sequencing (NGS) of DNA and RNA data Versions: 4.0.1-1 License: Apache License 2.0 https://docs.nvidia.com/clara/parabricks/4. 0.1/documentation/thirdpartysoftwarenotices.html Categories: Genomics, Healthcare, big data, pipelines ============================================================================== PGI compilers ============================================================================== Description: Compiler suite. Versions: 20.4 License: http://www.pgroup.com/doc/LICENSE.txt Categories: Compiler, development, debugger, profiler ============================================================================== plink ============================================================================== Description: PLINK a whole genome association analysis toolset. Versions: 1.9; 2.0; 2.3a; 2.3a3; 2.3dev; 2.4a4 License: GPLv3 Categories: Bioinformatics ============================================================================== PROJ ============================================================================== Description: PROJ is a generic coordinate transformation software. Versions: 9.0.0 License: MIT Categories: GIS, Library ============================================================================== py-macs2 ============================================================================== Description: MACS2 Model-based Analysis of ChIP-Seq Versions: 2.2.4 License: N/A Categories: N/A ============================================================================== py-weblogo ============================================================================== Description: WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. Versions: 3.7.12 License: N/A Categories: N/A ============================================================================== PyArrow ============================================================================== Description: In-memory analytics for use within Python. Versions: 8.0.0 License: https://github.com/apache/arrow/blob/master/LICENSE.txt Categories: Programming, python ============================================================================== Python ============================================================================== Description: Python is a general purpose programming language Versions: 3.10.4; 3.9.12 License: https://docs.python.org/3/license.html Categories: Programming, language ============================================================================== PyTorch ============================================================================== Description: Python tensor library for deep learning. Versions: 1.12.1 License: https://pytorch.org/ Categories: Programming, python, machine learning, tensor, GPU ============================================================================== R ============================================================================== Description: R environment for statistical computing and graphics Versions: 4.2.0 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, graphics, big data, data science ============================================================================== r-seurat ============================================================================== Description: Tools for Single Cell Genomics Versions: 4.1.1 License: N/A Categories: N/A ============================================================================== raxml ============================================================================== Description: RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. Versions: 8.2.11; 8.2.12 License: N/A Categories: N/A ============================================================================== rclone ============================================================================== Description: rclone is a command line program to sync files and directories to and from many cloud storage providers Versions: 1.57.0 License: MIT License Categories: File transfer, Utilities ============================================================================== Rgeospatial ============================================================================== Description: A collection of R geospatial libraries Versions: 2022-08-18; 2023-04-25 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, graphics, big data, data science, geospatial, geography, spatial, map ============================================================================== rmats ============================================================================== Description: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. Versions: 4.0.2 License: N/A Categories: N/A ============================================================================== Ropenblas ============================================================================== Description: R OpenBLAS provides an optimized library for faster linear algebra computations. Versions: 4.2.0 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, linear algebra, big data, data science ============================================================================== RStudio Server ============================================================================== Description: RStudio Desktop is a graphichal user interface for R. Versions: 2022.07.1; 2022.07.2 License: AGPL v3 Categories: Statistics, graphics, big data, data science, IDE ============================================================================== Rtidyverse ============================================================================== Description: R Tidyverse environment for statistical computing and graphics Versions: 4.2.0 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, graphics, big data, data science, tidyverse ============================================================================== saige ============================================================================== Description: SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model Versions: 0.44.6.4; 1.1.6.2 License: BSD Simplified 2-Clause Categories: Bioinformatics ============================================================================== salmon ============================================================================== Description: Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Versions: 1.9.0 License: N/A Categories: N/A ============================================================================== samtools ============================================================================== Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format Versions: 1.13; 1.9 License: N/A Categories: N/A ============================================================================== SAS ============================================================================== Description: SAS statistical system software. Versions: 9.4-TS1M7 License: Not available Categories: Statistics, econometrics ============================================================================== SciPy ============================================================================== Description: Scientific libraries for use within Python. Versions: 1.8.0 License: https://github.com/scipy/scipy Categories: Programming, python, solver ============================================================================== seqkit ============================================================================== Description: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang. Versions: 2.3.0 License: N/A Categories: N/A ============================================================================== Singularity ============================================================================== Description: Program for running containerized applications Versions: 3.10.4; 3.11.1 License: https://github.com/sylabs/singularity/blob/master/LICENSE.md Categories: Container, docker, reproducible research ============================================================================== spades ============================================================================== Description: SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. Versions: 3.15.5 License: N/A Categories: N/A ============================================================================== spark ============================================================================== Description: Apache Spark is a unified analytics engine for large-scale data processing Versions: 3.2.1 License: Apache, https://www.apache.org/licenses/LICENSE-2.0 Categories: Statistics, big data, data science ============================================================================== sratoolkit ============================================================================== Description: The NCBI SRA Toolkit enables reading ('dumping') of sequencing files from the SRA database and writing ('loading') files into the .sra format. Versions: 2.10.9 License: N/A Categories: N/A ============================================================================== star ============================================================================== Description: STAR is an ultrafast universal RNA-seq aligner. Versions: 2.7.6a License: N/A Categories: N/A ============================================================================== Stata/MP ============================================================================== Description: Statistical analysis software. Versions: 17 License: http://www.stata.com/order/end-user-license-agreement/ Categories: Statistics, econometrics ============================================================================== Stata/SE ============================================================================== Description: Statistical analysis software. Versions: 17 License: http://www.stata.com/order/end-user-license-agreement/ Categories: Statistics, econometrics ============================================================================== stringtie ============================================================================== Description: Transcript assembly and quantification for RNA-Seq Versions: 2.2.1; 2.1.7 License: GPLv2 Categories: Bioinformatics ============================================================================== subread ============================================================================== Description: a tool kit for processing next-gen sequencing data Versions: 1.6.0 License: GPLv2 Categories: Bioinformatics ============================================================================== szip ============================================================================== Description: Szip is a compression library used with HDF5. Versions: 2.1.1 License: https://www.hdfgroup.org/doc_resource/SZIP/ Categories: Utility, compression ============================================================================== tabix ============================================================================== Description: A useful tool that indexes large .vcf files Versions: 0.2.6 License: GPLv2 Categories: Bioinformatics ============================================================================== TBB ============================================================================== Description: Intel Thread Building Blocks. Versions: 2022.1.2 License: https://software.intel.com/en-us/articles/end-user-license- agreement Categories: Library, development, core, thread ============================================================================== TensorFlow ============================================================================== Description: Machine learning platform for use within Python. Versions: 2.7.0 License: Apache License 2.0 Categories: Programming, machine learning library, python ============================================================================== tmux ============================================================================== Description: Terminal multiplexer Versions: 3.3a License: https://opensource.org/licenses/ISC Categories: Terminal, multiplex ============================================================================== TractSeg ============================================================================== Description: Tool for fast and accurate white matter bundle segmentation from Diffusion MRI. Versions: 2.8 License: GPLv2 Categories: Bioinformatics ============================================================================== trimgalore ============================================================================== Description: Trim Galore! is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. Versions: 0.6.7 License: N/A Categories: N/A ============================================================================== trimmomatic ============================================================================== Description: Trimmomatic: A flexible read trimming tool for Illumina NGS data Versions: 0.36 License: GNU GPL v3 Categories: Bioinformatics, Sequencing ============================================================================== use.own ============================================================================== Description: Module to add personal module directory to module path. Versions: False License: None Categories: utility ============================================================================== valgrind ============================================================================== Description: An instrumentation framework for building dynamic analysis. Versions: 3.20.0 License: N/A Categories: N/A ============================================================================== Yasm ============================================================================== Description: Yasm assembler. Versions: 2.15.05 License: https://www.nasm.us/ Categories: assembler, programming ==============================================================================