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http://ranger.sourceforge.net/

Software for a multi-purpose ChIP Seq peak caller.

Proper citation: PeakRanger (RRID:SCR_010863) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS).

Proper citation: RRBSMAP (RRID:SCR_010864) Copy   

•   Source: SciCrunch Registry

http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS

An algorithm that allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity.

Proper citation: SIPeS (RRID:SCR_010865) Copy   

•   Source: SciCrunch Registry

http://www.math.miami.edu/~vhower/tpic.html

A software for determining DNA/protein binding sites from a ChIP-Seq experiment.

Proper citation: T-PIC (RRID:SCR_010867) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://pages.cs.wisc.edu/~kliang/DBChIP/

Detects differential binding of transcription factors with ChIP-seq.

Proper citation: DBChIP (RRID:SCR_010872) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://erne.sourceforge.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.aldevron.com/

Contract manufacturing services company, specializing in plasmid DNA manufacturing, protein services and antibody development.Producesg high quality plasmid DNA, proteins, enzymes, antibodies, and other biologicals in support of clients objectives.

Proper citation: Aldevron (RRID:SCR_011017) Copy   

•   Source: SciCrunch Registry

http://www.mrc.ac.uk/Fundingopportunities/index.htm

The Medical Research Council is a publicly-funded organization dedicated to improving human health. We support research across the entire spectrum of medical sciences, in universities and hospitals, in our own units, centers and institutes in the UK, and in our units in Africa.

Proper citation: Medical Research Council (RRID:SCR_011018) Copy   

•   Source: SciCrunch Registry

http://www.ics-mci.fr/en/

Research infrastructure for generation of new mouse models,being therefore the most important transgenic mouse production unit in France.

Proper citation: Mouse Clinical Institute; Alsace; France (RRID:SCR_011021) Copy   

•   Source: SciCrunch Registry

https://www.cayetano.edu.pe/cayetano/es/

Private nonprofit university located in Lima, Peru. It was named in honor of Cayetano Heredia, one of the eminent Peruvian physicians of the 19th century. The university is overseen by a board of trustees and is not owned by any private or state entity.

Proper citation: Cayetano Heredia University; Lima; Peru (RRID:SCR_011142) Copy   

•   Source: SciCrunch Registry

http://www.cgu.edu.tw/bin/home.php?Lang=en

Chang Gung University is a private university in Guishan District, Taoyuan City, Taiwan.

Proper citation: Chang Gung University; Taoyuan; Taiwan (RRID:SCR_011149) Copy   

•   Source: SciCrunch Registry

http://www.baylor.edu/

Private Baptist research university in Waco, Texas. Baylor was chartered in 1845 by the last Congress of the Republic of Texas.

Proper citation: Baylor University; Texas; USA (RRID:SCR_011029) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.genomics.cn/en/

Citizen-managed, non-profit research institution that uses genomics to benefit the human race. BGI (which includes both private non-profit research institutes and sequencing application commercial units) and its affiliated offshoots, BGI Americas and BGI Europe, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, to support a variety of healthcare, agricultural, environmental and related applications. BGI currently comprises of 4 regions: BGI China (Mainland), BGI Asia Pacific, BGI Americas (North and South America) and BGI Europe (Europe and Africa). Relying on advanced high-throughput sequencing technology, a highly efficient data analysis capability, uniquely rich biological resources, and a multidisciplinary scientific research system, BGI can provide innovative support for global communities, novel opportunities for researchers, and a regionally tailored application services in the fields of healthcare, agriculture and the environment.

Proper citation: BGI; Shenzhen; China (RRID:SCR_011114) Copy   

•   Source: SciCrunch Registry