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

DOI: 10.18129/B9.bioc.csaw    

This is the development version of csaw; for the stable release version, see csaw.

ChIP-Seq Analysis with Windows

Bioconductor version: Development (3.6)

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 csaw Vignette
PDF csawUserGuide.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.11.4
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License GPL-3
Depends R (>= 3.4), GenomicRanges, SummarizedExperiment(>= 1.2.0), BiocParallel
Imports Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, BiocGenerics, Rhtslib, stats, Rcpp
LinkingTo Rhtslib, zlibbioc, Rcpp
Suggests org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me diffHic
Suggests Me
Build Report  

Package Archives

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

Source Package csaw_1.11.4.tar.gz
Windows Binary csaw_1.11.4.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) csaw_1.11.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/csaw
Package Short Url http://bioconductor.org/packages/csaw/
Package Downloads Report Download Stats

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