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http://software.big.ac.cn/MeRIP-PF.html
A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.
Proper citation: MeRIP-PF (RRID:SCR_010904) Copy
https://code.google.com/p/bsolana/
An approach for the analysis of two-base encoding bisulfite sequencing data.
Proper citation: B-SOLANA (RRID:SCR_010905) Copy
https://code.google.com/p/batmeth/
Improved mapper for bisulfite sequencing reads on DNA methylation.
Proper citation: BatMeth (RRID:SCR_010906) Copy
You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.
Proper citation: QUMA (RRID:SCR_010907) 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
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.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
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
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