last updated: Thursday, 25-Apr-2024 12:00:03 EDT
Abaqus ============================================================================== Description: Abaqus FEA product suite for engineering problems. Versions: 2022 License: Non-commercial research, Academic Institution License Agreement Categories: FEA, dynamic vibration, impact/crash, thermal coupling ============================================================================== Absoft Pro Fortran ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu] Absoft Pro Fortran Compiler Versions: 18.0.2 License: http://www.absoft.com/literature/Absoftlicense.pdf Categories: fortran, compiler, f95/f90 ============================================================================== 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 ============================================================================== ANSYS ============================================================================== Description: ANSYS is a finite element simulation tool for multiphysics simulations. Versions: 21.2 License: Academic Research Categories: CFD, FEM, finite element, multiphysics ============================================================================== ANSYS EM ============================================================================== Description: ANSYS EM: HFSS and Maxwell Versions: 21.2 License: Academic Research Categories: EM, CEM, HFSS, Maxwell ============================================================================== 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: 0.15.6; 0.16.0 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 ============================================================================== 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 ============================================================================== bcl-convert ============================================================================== Description: Converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. Versions: 4.2.4 License: GPLv2 Categories: Bioinformatics ============================================================================== 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 ============================================================================== bowtie ============================================================================== Description: Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Versions: 1.3.0 License: N/A Categories: N/A ============================================================================== 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 ============================================================================== Bridger Assembler ============================================================================== Description: Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. Versions: 2014.12.01 License: GNU GENERAL PUBLIC LICENSE Categories: Bioinformatics, Genomics, Healthcare, big data ============================================================================== 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 ============================================================================== cellpose ============================================================================== Description: cellpose is an anatomical segmentation algorithm written in Python 3. Versions: 2.1.1 License: https://github.com/MouseLand/cellpose/blob/main/LICENSE Categories: Biology, deep-learning, biomedical, cell segmentation, image analysis ============================================================================== cellranger ============================================================================== Description: Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output Versions: 7.1.0; 7.2.0; 8.0.0 License: GPLv2 Categories: Bioinformatics ============================================================================== cellrangerARC ============================================================================== Description: a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data Versions: 2.0.2 License: GPLv2 Categories: Bioinformatics ============================================================================== cellrangerATAC ============================================================================== Description: a set of analysis pipelines that process Chromium Single Cell ATAC data Versions: 2.1.0 License: GPLv2 Categories: Bioinformatics ============================================================================== 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 ============================================================================== code-server ============================================================================== Description: Run VS Code on any machine anywhere and access it in the browser. Versions: 4.8.3 License: MIT Categories: file management, software development, scripting, IDE. ============================================================================== 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: http://docs.nvidia.com/cuda/eula 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 ============================================================================== 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 ============================================================================== fastqc ============================================================================== Description: A quality control tool for high throughput sequence data. Versions: 0.11.5; 0.11.9; 0.12.1 License: N/A Categories: N/A ============================================================================== FEKO ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu] Feko is a computational electromagnetics software. Versions: 2021.2; 2022.1 License: https://caen.engin.umich.edu/software/licensing/ Categories: computational electromagnetics ============================================================================== FFMPEG ============================================================================== Description: FFMPEG is a complete, cross-platform solution to record, convert and stream audio and video. Versions: 4.4.2; 5.1.2; 6.0.0 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 ============================================================================== 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; 4.1.0.0; 4.2.2.0 License: Broad Institute Software License Agreement Categories: Bioinformatics ============================================================================== Gaussian ============================================================================== Description: Gaussian is an electronic structure program. Versions: 09-revD01; 16-revA03-avx2; 16-revC01-avx2 License: Academic, noncommercial research and instructional use only. Categories: electronic structure, molecular ============================================================================== gcc ============================================================================== Description: GNU compiler suite Versions: 10.3.0; 11.2.0; 13.2.0 License: GPL Categories: Compiler, programming, development ============================================================================== GDAL ============================================================================== Description: GDAL is a translator library for raster and vector geospatial data formats. Versions: 3.5.1; 3.8.3 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; 3.12.1 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 ============================================================================== globus-cli ============================================================================== Description: The CLI provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. Versions: 3.4.0 License: N/A Categories: Data movement ============================================================================== 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 ============================================================================== GSL ============================================================================== Description: GNU scientific libraries Versions: 2.7 License: GPL Categories: Programming, library, mathematics ============================================================================== gst-libav ============================================================================== Description: GStreamer plugin for the libav* library. Versions: 1.16.1 License: https://github.com/GStreamer/gst-libav?tab=LGPL-2.1-1-ov- file#readme Categories: multimedia ============================================================================== Gurobi ============================================================================== Description: Gurobi optimization problem solver. Versions: 10.0.2; 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 ============================================================================== HELIOS ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] HELIOS Generalized Geometry Lattice Analysis package. Includes Casmo and Simulate from teh Studsvik suite. Versions: 1.12; 1.12-sing; 1.13 License: N/A Categories: Geometry Lattice Analysis, hexagonal VVER reactors, non-LWR lattices ============================================================================== 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: 1.13; 1.9 License: N/A Categories: N/A ============================================================================== 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 ============================================================================== ilastik ============================================================================== Description: Interactive learning and segmentation toolkit. Versions: 1.4.0 License: https://www.ilastik.org/license.html Categories: Machine learning, image classification, image analysis. ============================================================================== 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; 5.3.0 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 ============================================================================== 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: 1.10.2; 1.7.2 License: MIT Licenses Categories: Programming ============================================================================== Lahey Fortran ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu] Lahey Fortran - f95/f90 fortran compiler Versions: 8.1b License: http://www.lahey.com/docs/lfpro73help/f95gslicense.htm Categories: fortran, compiler, f95/f90 ============================================================================== 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 ============================================================================== Linaro Forge ============================================================================== Description: Parallel debugging and profiling tools, DDT and MAP. Versions: 23.0.3 License: Not available Categories: Programming, profiler, debugger, performance ============================================================================== Mathematica ============================================================================== Description: Mathematical and technical computing package. Versions: 12.3.1; 13.2.1 License: http://www.wolfram.com/legal/agreements/wolfram- mathematica.html Categories: Mathematics, symbolic algebra ============================================================================== Matlab ============================================================================== Description: Matlab programming environment. Versions: R2019b; R2021b; R2022b; R2023b 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 ============================================================================== 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 ============================================================================== MPlayer ============================================================================== Description: MPlayer is a free and open-source media player software that supports a wide variety of audio and video formats. It runs on multiple platforms including Linux, Windows, and macOS. Versions: 1.5 License: GNU General Public License version 2 Categories: media player, multimedia ============================================================================== MRtrix ============================================================================== Description: MRtrix provides a set of tools to perform various advanced diffusion MRI analyses. Versions: 3.0.3-dfd3360; 3.0.4 License: Mozilla Public License, http://mozilla.org/MPL/2.0/ Categories: fMRI, diffusion-weighted MRI, tractography, neuroimaging ============================================================================== nagf95 ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu] NAGWARE - f95/f90 fortran compiler Versions: 6.1-6120; 6.2-6214 License: file:///sw/pkgs/coe/c/nagf95/6.1-6120/lic_agr.txt Categories: fortran, compiler ============================================================================== Natural Bond Orbital (NBO) ============================================================================== Description: Computational chemistry program for the analysis of many- electron molecular wavefunctions. Versions: 7.0 License: (c) Copyright 1996-2018 Board of Regents of the University of Wisconsin System on behalf of the Theoretical Chemistry Institute. All rights reserved. Categories: Computational Chemistry, Quantum Chemistry, simulation. ============================================================================== 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 ============================================================================== NERS-CLASS-SW ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Software for NERS classses: mcc2-3, rebus, dif3d, twodant. Versions: 1.0 License: N/A Categories: Nuclear ============================================================================== NetCDF ============================================================================== Description: Libraries for creating and manipulating NetCDF files. Versions: 4.8.1; 4.6.2 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 ============================================================================== 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; 0.3.23 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; 4.1.6 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 ============================================================================== Parallel HDF5 (PHDF5) ============================================================================== Description: Parallel HDF5 data libraries and utilities. Versions: 1.12.1 License: https://www.hdfgroup.org/products/licenses.html Categories: Utility, programming, library ============================================================================== Paraview ============================================================================== Description: Paraview data analysis and visualization application. Versions: 5.12.0 License: http://www.paraview.org/paraview-license/ Categories: Visualization, data analysis ============================================================================== 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 License: GPLv3 Categories: Bioinformatics ============================================================================== Poetry ============================================================================== Description: Python packaging and dependency management. Versions: 1.6.1 License: https://github.com/python-poetry/poetry Categories: Programming, dependency management, python ============================================================================== PROJ ============================================================================== Description: PROJ is a generic coordinate transformation software. Versions: 9.0.0; 9.3.1 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; 3.11.5; 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; 2.0.1 License: https://pytorch.org/ Categories: Programming, python, machine learning, tensor, GPU ============================================================================== R ============================================================================== Description: R environment for statistical computing and graphics Versions: 4.2.0; 4.3.1 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; 2023-07-01 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; 4.3.1 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; 2023.06.1; 2023.09.1 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; 4.3.1 License: GPL, https://www.r-project.org/Licenses/ Categories: Statistics, graphics, big data, data science, tidyverse ============================================================================== 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 ============================================================================== ShellCheck ============================================================================== Description: ShellCheck, a static analysis tool for shell scripts Versions: 0.9.0 License: GPLv3 https://github.com/koalaman/shellcheck/blob/master/LICENSE Categories: Shell, Bash, Linter, static-analysis, developer-tools ============================================================================== 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 ============================================================================== spaceranger ============================================================================== Description: a set of analysis pipelines that process Visium spatial RNA- seq output and brightfield microscope images Versions: 2.0.1; 2.1.1; 3.0.0 License: GPLv2 Categories: Bioinformatics ============================================================================== Spack Package Manager ============================================================================== Description: A flexible package manager supporting multiple versions, configurations, platforms, and compilers. Versions: 0.21 License: Apache-2.0 Categories: Software Installation, compiling, package manager ============================================================================== 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 ============================================================================== 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; 2.9.6 License: N/A Categories: N/A ============================================================================== star ============================================================================== Description: STAR is an ultrafast universal RNA-seq aligner. Versions: 2.7.11a; 2.7.6a License: N/A Categories: N/A ============================================================================== Star-CCM+ ============================================================================== Description: Star-CCM+ is a CFD application that supports parallel processing. Versions: 17.04.007-R8; 17.04.007 License: Academic Research Categories: CFD ============================================================================== Stata/MP ============================================================================== Description: Statistical analysis software. Versions: 17; 18 License: http://www.stata.com/order/end-user-license-agreement/ Categories: Statistics, econometrics ============================================================================== Stata/SE ============================================================================== Description: Statistical analysis software. Versions: 17; 18 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 ============================================================================== 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 ============================================================================== 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 ============================================================================== Tecplot 360 & Tecplot Chorus ============================================================================== Description: Plotting and visualization software that gives full control over 2-D and 3-D plot parameters. Versions: 2022r1 License: N/A Categories: plotting, visualization ============================================================================== TensorFlow ============================================================================== Description: Machine learning platform for use within Python. Versions: 2.7.0 License: Apache License 2.0 Categories: Programming, machine learning library, python ============================================================================== TensorRT ============================================================================== Description: An SDK for high-performance deep learning inference. Versions: 11.8-v8.6.1 License: Apache License 2.0 Categories: Programming, Machine Learning, Tensorflow, Inference ============================================================================== tmux ============================================================================== Description: Terminal multiplexer Versions: 3.3a License: https://opensource.org/licenses/ISC Categories: Terminal, multiplex ============================================================================== 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 ============================================================================== Trinity ============================================================================== Description: Trinity assembles transcript sequences from Illumina RNA-Seq data. Versions: 2.15.1 License: https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/ master/LICENSE Categories: Bioinformatics, Assembly, Transcriptome ============================================================================== UCX ============================================================================== Description: Unified Communication X (UCX) Versions: 1.14.1 License: https://github.com/openucx/ucx?tab=License-1-ov-file#readme Categories: Communication ============================================================================== 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 ============================================================================== VASP ============================================================================== Description: [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu] VASP, The Vienna Ab initio simulation package, a plane wave electronic structure code. Versions: 5.4.1.05Feb16.p2.b; 5.4.4.18Apr17; 5.4.4.18Apr17.p1; 5.4.4.18Apr17.vaspsol.170729; old-4.6.36Feb09; old-5.2.12.11Nov2011; old-5.3.2.13Sep2012; old-5.3.3.18Dec2012; old-5.3.5.31Mar2014; old-5.3.5.31Mar2014wannier90v12 License: https://www.vasp.at/index.php/faqs Categories: electronic structure code, molecular dynamics ============================================================================== Yasm ============================================================================== Description: Yasm assembler. Versions: 2.15.05; 1.3.0 License: https://www.nasm.us/ Categories: assembler, programming ==============================================================================