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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.mimg.ucla.edu/faculty/xing/glimmps/

Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data.

Proper citation: GLiMMPS (RRID:SCR_001787) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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://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://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

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

http://sourceforge.net/projects/foursig/

A suite of software programs for analyzing and visualizing 4C-seq data.

Proper citation: fourSig (RRID:SCR_000516) Copy   

•   Source: SciCrunch Registry

https://github.com/GregoryFaust/samblaster

Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

Proper citation: SAMBLASTER (RRID:SCR_000468) Copy   

•   Source: SciCrunch Registry

http://www.tapyr.net/

An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.

Proper citation: TAPyR (RRID:SCR_000588) Copy   

•   Source: SciCrunch Registry

http://open-ms.sourceforge.net/documentation/knime-integration/

A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.

Proper citation: TOPPAS (RRID:SCR_000533) Copy   

•   Source: SciCrunch Registry

http://mendel.stanford.edu/SidowLab/downloads/gerp/

Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERP (RRID:SCR_000563) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/mutect

Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Proper citation: MuTect (RRID:SCR_000559) Copy   

•   Source: SciCrunch Registry

http://thomsonreuters.com/metadrug/

A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Proper citation: MetaDrug (RRID:SCR_000461) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/reprever/?source=directory

Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number.

Proper citation: Reprever (RRID:SCR_000463) Copy   

•   Source: SciCrunch Registry