To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("csaw")

In most cases, you don't need to download the package archive at all.

csaw

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see csaw.

ChIP-seq analysis with windows

Bioconductor version: 3.0

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Author: Aaron Lun <alun at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>

Maintainer: Aaron Lun <alun at wehi.edu.au>

Citation (from within R, enter citation("csaw")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("csaw")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("csaw")
PDF R Script csaw Vignette
PDF csawUserGuide.pdf
PDF Reference Manual
Text NEWS

Details

biocViews Annotation, ChIPSeq, Coverage, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.0.7
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-3
Depends R (>= 3.1.0), GenomicRanges
Imports Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, GenomicAlignments, S4Vectors, IRanges, GenomeInfoDb
LinkingTo
Suggests org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source csaw_1.0.7.tar.gz
Windows Binary csaw_1.0.7.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) csaw_1.0.7.tgz
Mac OS X 10.9 (Mavericks) csaw_1.0.7.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/csaw/tree/release-3.0
Package Short Url http://bioconductor.org/packages/csaw/
Package Downloads Report Download Stats

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