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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
Public university in Perth, Western Australia, with campuses also in Singapore and Dubai. It began operations as the state's second university on 25 July 1973, and accepted its first undergraduate students in 1975.
Proper citation: Murdoch University; Perth; Australia (RRID:SCR_011037) Copy
http://ww2.odu.edu/~nxkim/nextpeak/
A software program to call peaks from ChIP-seq data for transcription factor binding sites.
Proper citation: NEXT-peak (RRID:SCR_010862) Copy
https://www.mju.ac.kr/sites/mjukr/intro/intro.html
Myongji University is private, Christian university founded in 1948 in South Korea. Provides higher education in fields of engineering, sciences and humanities.
Proper citation: Myongji University; Gyeonggi-do; South Korea (RRID:SCR_011038) Copy
http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
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
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
http://www.scienceexchange.com/facilities/ksf-labs
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022. KSF Labs is the virtual/real workshop(s).
Proper citation: KSF Labs (RRID:SCR_010987) Copy
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
Founded in 1995 with intention of making DNA sequencing and genotyping laboratory to provide DNA sequencing and genotyping services for academic institutions or for private companies.
Proper citation: Laragen (RRID:SCR_010989) Copy
http://www.scienceexchange.com/facilities/rutgers-university
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022.
Proper citation: Rutgers University Labs and Facilities (RRID:SCR_010990) Copy
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
https://app.scientist.com/providers/stamford-bioprocess-technologies
Located in Southern California, USA, Stamford Bioprocess Technologies provides bioprocess and related services for recombinant protein production.
Proper citation: Stamford Bioprocess Technologies (RRID:SCR_010992) 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://www.spiralgenetics.com/
Core facility which provides assistance in statistical analyses as well as in organization. Core facility offers two main analysis programs titled Spiral Genetics' BioGraph and Structural Variant Analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Spiral Genetics Incorporated (RRID:SCR_011048) 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://www.scienceexchange.com/facilities/iowa-state-university
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022.
Proper citation: Iowa State University Labs and Facilities (RRID:SCR_011052) 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
Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
Proper citation: HOMER (RRID:SCR_010881) Copy
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