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http://www.bioconductor.org/packages/2.11/bioc/html/ShortRead.html

Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.

Proper citation: ShortRead (RRID:SCR_006813) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/beadarray.html

Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Proper citation: beadarray (RRID:SCR_001314) Copy   

•   Source: SciCrunch Registry

http://proteinprophet.sourceforge.net/

Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.

Proper citation: ProteinProphet (RRID:SCR_000286) Copy   

•   Source: SciCrunch Registry

http://graphpad.com/

A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.

Proper citation: GraphPad (RRID:SCR_000306) Copy   

•   Source: SciCrunch Registry

https://posit.co/

Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).

Proper citation: RStudio (RRID:SCR_000432) Copy   

•   Source: SciCrunch Registry

https://github.com/SciLifeLab/facs

Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.

Proper citation: FACS (RRID:SCR_000055) Copy   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures.

Proper citation: GOLD (RRID:SCR_000188) Copy   

•   Source: SciCrunch Registry

http://www.ici.upmc.fr/cluego/

A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ClueGO (RRID:SCR_005748) Copy   

•   Source: SciCrunch Registry

http://www.jalview.org/

A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.

Proper citation: Jalview (RRID:SCR_006459) Copy   

•   Source: SciCrunch Registry

https://github.com/arq5x/bedtools2

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Proper citation: BEDTools (RRID:SCR_006646) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

Issue

https://reich.hms.harvard.edu/software

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.

Proper citation: Eigensoft (RRID:SCR_004965) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=cluster

Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.

Proper citation: Cluster (RRID:SCR_013505) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=survival

Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Proper citation: survival (RRID:SCR_021137) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=caret

Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

Proper citation: caret (RRID:SCR_021138) Copy   

•   Source: SciCrunch Registry

https://github.com/Illumina/strelka/

Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller.

Proper citation: Strelka2 (RRID:SCR_005109) Copy   

•   Source: SciCrunch Registry

http://www.utexas.edu

A major university

Proper citation: University of Texas at Austin; Texas; USA (RRID:SCR_005900) Copy   

•   Source: SciCrunch Registry

http://www.mediacy.com/imageproplus

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data.

Proper citation: Image Pro Plus (RRID:SCR_007369) Copy   

•   Source: SciCrunch Registry

http://qiime.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.

Proper citation: QIIME (RRID:SCR_008249) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/figtree

A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.

Proper citation: FigTree (RRID:SCR_008515) Copy   

•   Source: SciCrunch Registry