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https://code.google.com/p/gencat/
Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats.
Proper citation: genCAT (RRID:SCR_013220) Copy
http://sourceforge.net/projects/socs/
Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.
Proper citation: SOCS (RRID:SCR_013223) Copy
http://www.bioconductor.org/packages//2.10/bioc/html/aCGH.html
Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
Proper citation: aCGH (RRID:SCR_013232) Copy
http://sourceforge.net/projects/denovosolid/
Pipeline for small genome assembly using SOLiD sequencing technology.
Proper citation: DSP (RRID:SCR_013114) Copy
https://github.com/adaptivegenome/repeatseq
Software that determines genotypes for microsatellite repeats in high-throughput sequencing data.
Proper citation: RepeatSeq (RRID:SCR_013235) Copy
http://sourceforge.net/projects/tuxe/
Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically.
Proper citation: Tuxedo (RRID:SCR_013194) Copy
http://www.seqan.de/projects/microrazers/
A software tool optimized for mapping short RNAs onto a reference genome.
Proper citation: MicroRazerS (RRID:SCR_013316) Copy
http://archive.gersteinlab.org/proj/rnaseq/fusionseq/
A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.
Proper citation: FusionSeq (RRID:SCR_013329) Copy
http://seqtracs.sourceforge.net/
Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility.
Proper citation: SeqTRACS (RRID:SCR_013294) Copy
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
A scalable software pipeline for whole genome resequencing analysis.
Proper citation: Crossbow (RRID:SCR_013306) Copy
http://tomcatbackup.esat.kuleuven.be/inclusive/
A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
Proper citation: INCLUSive (RRID:SCR_013488) Copy
http://ctb.pku.edu.cn/main/SheGroup/Software/MED2.htm
A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method.
Proper citation: MED (RRID:SCR_013403) Copy
http://hannonlab.cshl.edu/Alta-Cyclic/main.html
An Illumina Genome-Analyzer (Solexa) base caller.
Proper citation: Alta-Cyclic (RRID:SCR_013373) Copy
http://cran.r-project.org/web/packages/DWD/
This software package provides the implementation of distance weighted discrimination (DWD) using an interior point method for the solution of second order cone programming problems.
Proper citation: DWD (RRID:SCR_008760) Copy
An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
Proper citation: RUM (RRID:SCR_008818) Copy
https://github.com/armintoepfer/QuasiRecomb/releases
A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.
Proper citation: QuasiRecomb (RRID:SCR_008812) Copy
http://cran.r-project.org/web/packages/isva/
An algorithm for feature selection in the presence of potential confounding factors.
Proper citation: isva (RRID:SCR_008772) Copy
http://cran.r-project.org/web/packages/svd/
Interfaces to various state-of-art SVD and eigensolvers.
Proper citation: svd (RRID:SCR_008805) Copy
Merging Two Gene Expression Studies via Cross Platform Normalization.
Proper citation: XPN (RRID:SCR_008845) Copy
http://tvap.genome.wustl.edu/tools/music/
A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MuSiC (RRID:SCR_008792) Copy
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