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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   

•   Source: SciCrunch Registry

https://github.com/adrlar/CanSNPer

Software that is a hierarchical genotype classifier of clonal pathogens.

Proper citation: CanSNPer (RRID:SCR_001980) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/denovoassembler/files/

Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.

Proper citation: Ray (RRID:SCR_001916) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

Proper citation: flowMap (RRID:SCR_002269) Copy   

•   Source: SciCrunch Registry

http://cakesomatic.sourceforge.net/

A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

Proper citation: Cake (RRID:SCR_002133) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/matchprot/

A pairwise protein structure alignment software.

Proper citation: Matchprot (RRID:SCR_002163) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.13/bioc/html/shinyTANDEM.html

Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.

Proper citation: shinyTANDEM (RRID:SCR_002169) Copy   

•   Source: SciCrunch Registry

http://pfs.nus.edu.sg/(S(dyrcwejlfws33vxe23zlvrf3))/CopyRightNotice.aspx?ReturnURL=%2fQueryInterface_V5_2.aspx

Search engine integrating various bio-informatic resources and algorithims to produce a one-stop resource for biologists to identify potentially functional SNPs. It caters to different groups of scientists interested in SNPs including those working in the following areas: * Whole-genome association studies * Gene-based association studies * Designing experiments to address the functionality of specific SNPs * Determining potentially functionally significant SNPs that are in LD with non-pfSNPs of interest. Users may add published SNP functions.

Proper citation: pfSNP (RRID:SCR_002167) Copy   

•   Source: SciCrunch Registry

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

Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples.

Proper citation: flowMatch (RRID:SCR_002283) Copy   

•   Source: SciCrunch Registry

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

Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.

Proper citation: flowMeans (RRID:SCR_002275) Copy   

•   Source: SciCrunch Registry

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

Package of software functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. Draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.

Proper citation: rmeta (RRID:SCR_002270) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/RankAggreg/

Software package that performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm.

Proper citation: RankAggreg (RRID:SCR_002225) Copy   

•   Source: SciCrunch Registry

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

Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework.

Proper citation: flowMerge (RRID:SCR_002224) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/2.11/bioc/html/flowPhyto.html

An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

Proper citation: flowPhyto (RRID:SCR_002183) Copy   

•   Source: SciCrunch Registry