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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://probemer.cs.loyola.edu

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://rnbeads.bioinf.mpi-inf.mpg.de/

An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RnBeads (RRID:SCR_010958) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/fastdma/

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.

Proper citation: FastDMA (RRID:SCR_010954) Copy   

•   Source: SciCrunch Registry

http://www.illumina.com/software/illumina_connect.ilmn

Software that estimates copy number and annotates regions with copy number variants(CNV).

Proper citation: CNVPartition (RRID:SCR_010925) Copy   

•   Source: SciCrunch Registry