ChIPseeker 1.22.0 – ChIP peak Annotation, Comparison & Visualization

ChIPseeker 1.22.0

:: DESCRIPTION

ChIPseeker is an R package for annotating ChIP-seq data analysis.

::DEVELOPER

Guangchuang YU,

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX
  • R
  • Bioconductor

:: DOWNLOAD

 ChIPseeker

:: 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.

CHIP-RNA-SEQPRO 1.1 – ChIP-RNA-sequencing-processing

CHIP-RNA-SEQPRO 1.1

:: 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

  • Linux
  • R package

:: DOWNLOAD

   CHIP-RNA-SEQPRO

:: MORE INFORMATION

PeakFinder 1.0 – Find Cohesin Binding Sites in Yeast ChIP Microarray Data

PeakFinder 1.0

:: DESCRIPTION

PeakFinder program was developed to find cohesin binding sites represented by the peaks in yeast chromatin immunoprecipitation (ChIP) microarray data, but can be applied to plot any measurement against a parameter such as genome coordinate, to interactively analyze the measurement plot, and to annotate the peaks on the basis of local properties of the curve.

::DEVELOPER

Earl F. Glynn

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PeakFinder

:: MORE INFORMATION

Citation

Glynn EF, Megee PC, Yu H-G, Mistrot C, Unal E, et al. (2004)
Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae.
PLoS Biol 2(9): e259. doi:10.1371/journal.pbio.0020259

ChIPseek – Web-based tool for ChIP data analysis

ChIPseek

:: DESCRIPTION

ChIPseek is a web-based tool for ChIP (Chromatin Immunoprecipitation) data analysis providing summary statistics in graphs and offering several commonly demanded analyses. ChIPseek can provide statistical summary of the dataset including histogram of peak length distribution, histogram of distances to the nearest transcription start site (TSS), and pie chart (or bar chart) of genomic locations for users to have a comprehensive view on the dataset for further analysis.

::DEVELOPER

Chang Gung Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jun 30;15:539. doi: 10.1186/1471-2164-15-539.
ChIPseek, a web-based analysis tool for ChIP data.
Chen TW, Li HP, Lee CC, Gan RC, Huang PJ, Wu TH, Lee CY, Chang YF, Tang P

PASS 2 – Control the FDR level in ChIP data analysis

PASS 2

:: 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

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASS

:: 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.

COCAS 2.4 – ChIP on Chip Analysis Suite

COCAS 2.4

:: 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

Lab. Pierre FERRIER

:: 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.