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http://mesquiteproject.org/packages/chromaseq/

A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap.

Proper citation: Chromaseq (RRID:SCR_005587) Copy   

•   Source: SciCrunch Registry

https://github.com/phe-bioinformatics/snp-search/tree/master/test_data

A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses.

Proper citation: snp-search (RRID:SCR_005618) Copy   

•   Source: SciCrunch Registry

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

A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input.

Proper citation: MAGENTA (RRID:SCR_003422) Copy   

•   Source: SciCrunch Registry

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

Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software.

Proper citation: NAPPA (RRID:SCR_003419) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/fade/

A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms.

Proper citation: FadE (RRID:SCR_003448) Copy   

•   Source: SciCrunch Registry

http://www.compgen.org/tools/metagen

Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.

Proper citation: metagen (RRID:SCR_003443) Copy   

•   Source: SciCrunch Registry

http://ims.cochrane.org/revman/about-revman-5

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RevMan (RRID:SCR_003581) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.bc.edu/marthlab/wiki/index.php/PyroBayes

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines.

Proper citation: PyroBayes (RRID:SCR_003757) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/RAREMETAL

A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.

Proper citation: RAREMETAL (RRID:SCR_003573) Copy   

•   Source: SciCrunch Registry

http://www.exelixis-lab.org/software.html

Software for an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

Proper citation: PEAR (RRID:SCR_003776) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqexpress/

A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.

Proper citation: SeqExpress (RRID:SCR_004013) Copy   

•   Source: SciCrunch Registry

http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.

Proper citation: CisGenome (RRID:SCR_001558) Copy   

•   Source: SciCrunch Registry

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

Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

Proper citation: vsn (RRID:SCR_001459) Copy   

•   Source: SciCrunch Registry

https://github.com/nolanlab/cytospade

Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.

Proper citation: CytoSPADE (RRID:SCR_001457) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/baccontigeditor/

A simple sequence alignment editing tool, written in Java.

Proper citation: BACContigEditor (RRID:SCR_001617) Copy   

•   Source: SciCrunch Registry

https://github.com/CollasLab/edd

A ChIP-seq peak caller for detection of megabase domains of enrichment.

Proper citation: Enriched Domain Detector (RRID:SCR_001693) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CNVrd2.html

A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

Proper citation: CNVrd2 (RRID:SCR_001723) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.13/bioc/html/sSeq.html

Software package to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.

Proper citation: sSeq (RRID:SCR_001719) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.dreamhosters.com/?page_id=113#Genomic_Protein_Sequence_Analysis

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R software package for detecting and correcting biases in RNA-Sequencing data.

Proper citation: RNASeqBias (RRID:SCR_001739) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.med.yale.edu/group/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments.

Proper citation: pairedBayes (RRID:SCR_001738) Copy   

•   Source: SciCrunch Registry