:: DESCRIPTION
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites.
::DEVELOPER
Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ChIPseeker is an R package for annotating ChIP-seq data analysis.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
Yu G, Wang LG, He QY.
Bioinformatics. 2015 Mar 11. pii: btv145.
:: DESCRIPTION
PASS (Poisson Approximation for Statistical Significance) is a software that can accurately control the FDR level in ChIP data analysis. The method is designed for detecting transcription factor binding, and may not work well for wide spread signals such as nucleopositioning data. If the data is from ChIP-seq, you need to convert each ChIP-seq value into z-scores before using this program.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2008 Dec 15;24(24):2825-31. Epub 2008 Oct 25.
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays.
Zhang Y.
:: DESCRIPTION
CoCAS is a standalone Chromatin immunoprecipitation microarray (ChIP-on-chip) analysis application. It has been designed to be used primarily on Agilent microarrays scanned with an Agilent scanner.
CoCAS can readily be used on the latest generation of Agilent high-density arrays. Unlike other tools available, Cocas allows dye-swap, replicate correlation and connects easily with other software (genome browsers and peak detection). The peak detection methods implemented in CoCAS can be used for any set of data including ChIP-Seq data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
COCAS for Win ; for Mac ; for Linux
:: MORE INFORMATION
Citation:
Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P (2009). CoCAS: A ChIP-on-chip Analysis Suite. Bioinformatics 25: 954-5.
