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https://software.broadinstitute.org/gatk/

A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)

Proper citation: GATK (RRID:SCR_001876) Copy   

•   Source: SciCrunch Registry
  

http://www.agcol.arizona.edu/software/tcw/

Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.

Proper citation: TCW (RRID:SCR_001875) Copy   

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https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

Software tool to visualize and analyse high throughput mapped sequence data.

Proper citation: SeqMonk (RRID:SCR_001913) Copy   

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http://victorian-bioinformatics-consortium.github.io/degust/

An interactive web tool for visualizing differential gene expression data.

Proper citation: Degust (RRID:SCR_001878) Copy   

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

Software that provides utilities for flow cytometry data.

Proper citation: flowUtils (RRID:SCR_001879) Copy   

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https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

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https://github.com/JialiUMassWengLab/TEMP

Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.

Proper citation: TEMP (RRID:SCR_001788) Copy   

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https://github.com/uci-cbcl/EXTREME

A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data.

Proper citation: EXTREME (RRID:SCR_001821) Copy   

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http://www.megabionet.org/atpid/webfile/

Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

Proper citation: Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/openadam/

A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms.

Proper citation: openADAM (RRID:SCR_002018) Copy   

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

Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.

Proper citation: flowTrans (RRID:SCR_002093) Copy   

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http://www.broadinstitute.org/mpg/snap/

A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots

Proper citation: SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) Copy   

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https://github.com/nicolazzie/AffyPipe

An open-source software pipeline for Affymetrix Axiom genotyping workflow.

Proper citation: AffyPipe (RRID:SCR_002032) Copy   

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https://github.com/adrlar/CanSNPer

Software that is a hierarchical genotype classifier of clonal pathogens.

Proper citation: CanSNPer (RRID:SCR_001980) Copy   

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http://sourceforge.net/projects/dmetanalyzer/

Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way.

Proper citation: DMET-Analyzer (RRID:SCR_002030) Copy   

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http://snver.sourceforge.net/

Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

Proper citation: SNVer (RRID:SCR_002061) Copy   

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http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPSeq.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ChIPSeq Peak Finder (RRID:SCR_002081) Copy   

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https://github.com/homopolymer/PyroTools/

A software program to call short indels and SNPs for Ion Torrent and 454 data.

Proper citation: PyroHMMvar (RRID:SCR_002073) Copy   

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https://sites.google.com/site/emesbioinformatics/group-software/nimbl

MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.

Proper citation: NIMBL (RRID:SCR_000482) Copy   

•   Source: SciCrunch Registry
  

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

Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.

Proper citation: iBMQ (RRID:SCR_000481) Copy   

•   Source: SciCrunch Registry