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http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPDiff.htm
Provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2).
Proper citation: ChIPDiff Library Comparison (RRID:SCR_010871) Copy
http://biodoop-seal.sourceforge.net/
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
Proper citation: SEAL (RRID:SCR_010914) Copy
http://www.mhh.de/acghtool.html
A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs.
Proper citation: aCGHtool (RRID:SCR_010915) Copy
https://earray.chem.agilent.com/cghanalytics/index.html
A comprehensive design and analysis tool for setting up and interpreting your microarray experiments.
Proper citation: Agilent Genomic Workbench (RRID:SCR_010918) Copy
http://pages.cs.wisc.edu/~kliang/DBChIP/
Detects differential binding of transcription factors with ChIP-seq.
Proper citation: DBChIP (RRID:SCR_010872) Copy
http://cran.r-project.org/web/packages/DIME/index.html
R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
Proper citation: DIME (RRID:SCR_010874) Copy
http://www.cs.ucf.edu/~xiaoman/ChIPModule/ChIPModule.html
A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data.
Proper citation: ChIPModule (RRID:SCR_010877) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
Proper citation: ERNE (RRID:SCR_010912) Copy
http://fureylab.web.unc.edu/software/fseq/
A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.
Proper citation: F-Seq (RRID:SCR_010880) Copy
http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer
An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data.
Proper citation: ABySS-Explorer (RRID:SCR_010980) Copy
http://dnptrapper.sourceforge.net/
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Proper citation: DNPTrapper (RRID:SCR_010981) Copy
http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors.
Proper citation: Hawkeye (RRID:SCR_010982) Copy
http://sourceforge.net/projects/dical-ibd/
Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences.
Proper citation: diCal-IBD (RRID:SCR_012111) Copy
http://sourceforge.net/projects/ionwinze/
Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.
Proper citation: Ionwinze (RRID:SCR_012115) Copy
http://sourceforge.net/projects/genosight/
An adaptive imaging cytometry software environment.
Proper citation: GenoSIGHT (RRID:SCR_012119) Copy
https://github.com/stoeckli/MSImageViewer
Software for the conversion of data acquired with the FlashQuant (MALDI version of ABSciex 4000) into MS images.
Proper citation: MSImageViewer (RRID:SCR_012121) Copy
https://code.google.com/p/cell-motility/
An open source Java application that provides a clear and concise analysis workbench for large amounts of cell motion data.
Proper citation: Cell motility (RRID:SCR_012120) Copy
https://code.google.com/p/glycanbuilder/
An intuitive and flexible software tool for building and displaying glycan structures.
Proper citation: GlycanBuilder (RRID:SCR_012123) Copy
https://code.google.com/p/glycresoft/
A software package for automated recognition of glycans from LC/MS data.
Proper citation: GlycReSoft (RRID:SCR_012122) Copy
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