chipseq

chipseq: A package for analyzing chipseq data

Bioconductor version: 2.6

Tools for helping process short read data for chipseq experiments

Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao

Maintainer: Biocore Team c/o BioC user list <bioconductor at stat.math.ethz.ch>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("chipseq")

To cite this package in a publication, start R and enter:

    citation("chipseq")

Documentation

PDF R Script A Sample ChIP-Seq analysis workflow
PDF   Reference Manual

Details

biocViews Infrastructure, Bioinformatics
Depends methods, IRanges(>= 1.6.10), GenomicRanges(>= 1.0.7), BSgenome, ShortRead
Imports BSgenome, GenomicRanges, IRanges, lattice, methods, ShortRead, stats
Suggests GenomicFeatures, GenomicFeatures.Mmusculus.UCSC.mm9, GenomicFeatures.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9
System Requirements
License Artistic-2.0
URL
Depends On Me PICS
Imports Me
Suggests Me oneChannelGUI
Version 0.4.1
Since Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source chipseq_0.4.1.tar.gz
Windows Binary chipseq_0.4.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary chipseq_0.4.1.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center