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http://www.sanger.ac.uk/resources/software/cnd/
A program to detect copy number variants from short read sequence data.
Proper citation: CnD (RRID:SCR_010818) Copy
http://mendel.stanford.edu/SidowLab/downloads/MAPP/
Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MAPP (RRID:SCR_010775) Copy
http://www.ngsbicocca.org/html/ceqer.html
A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.
Proper citation: CEQer (RRID:SCR_010813) Copy
http://bg.upf.edu/group/projects/oncodrive-fm.php
An approach to uncover driver genes or gene modules.
Proper citation: Oncodrive-fm (RRID:SCR_010781) Copy
https://sites.google.com/site/vibansal/software/crisp
A software program to detect SNPs and short indels from pooled sequencing data generated using next-generation sequencing instruments.
Proper citation: CRISP (RRID:SCR_010759) Copy
https://github.com/ice91/CloudBrush
A De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework.
Proper citation: CloudBrush (RRID:SCR_010751) Copy
http://www.bcgsc.ca/platform/bioinfo/software/ssake
Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.
Proper citation: SSAKE (RRID:SCR_010753) Copy
https://code.google.com/p/comb/
A software package designed for the downstream analysis of short read mapping data produced by the ABI SOLiD and Illumina sequencing platforms.
Proper citation: ComB (RRID:SCR_010757) Copy
http://www.embl.de/~korbel/CopySeq/
A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.
Proper citation: CopySeq (RRID:SCR_010758) Copy
https://github.com/ekg/freebayes
A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.
Proper citation: FreeBayes (RRID:SCR_010761) Copy
https://code.google.com/p/balony/
Image analysis and data inspection software for agar plates generated in high-throughput yeast genetics and genomics experiments.
Proper citation: balony (RRID:SCR_010968) Copy
http://www.bioinformatics.org/oligofaktory/
A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more��
Proper citation: OligoFaktory (RRID:SCR_010962) Copy
http://probemaker.sourceforge.net/
A Java software aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.
Proper citation: ProbeMaker (RRID:SCR_010964) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 1, 2014, A web-based software tool that enables selecting optimal oligos for PCR applications and multiplex detection.
Proper citation: PROBEmer (RRID:SCR_010965) Copy
http://www.stat.wisc.edu/~chungdon/dpeak/
A high resolution transcription factor binding site (TFBS) identification (deconvolution) algorithm. dPeak implements a probabilistic model that accurately describes ChIP-exo and ChIP-Seq data generation process for both the SET and PET assays.
Proper citation: dPeak (RRID:SCR_010855) Copy
http://bioinfo-out.curie.fr/projects/micsa/
A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris).
Proper citation: MICSA (RRID:SCR_010860) Copy
http://ceas.cbi.pku.edu.cn/index.html
Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CEAS (RRID:SCR_010946) Copy
http://www.cebitec.uni-bielefeld.de/comics/index.php/emma
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 17, 2017. A MAGE-compliant software platform for the collaborative analysis and integration of microarray data.
Proper citation: EMMA2 (RRID:SCR_010940) Copy
http://sourceforge.net/projects/xdrawchem/
A drawing software application designed for drawing and analyzing chemical structures and reactions.
Proper citation: XDrawChem (RRID:SCR_010941) Copy
http://genetics.emory.edu/research/?assetID=2087
A GUI software package for analysis of DNA methylation microarray data.
Proper citation: MethLAB (RRID:SCR_010957) Copy
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