csaw

DOI: 10.18129/B9.bioc.csaw    

ChIP-Seq Analysis with Windows

Bioconductor version: Release (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>

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	1.12.0
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 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, vulcan
Suggests Me
Build Report

Package Archives

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

Source Package	csaw_1.12.0.tar.gz
Windows Binary	csaw_1.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	csaw_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/csaw
Package Short Url	http://bioconductor.org/packages/csaw/
Package Downloads Report	Download Stats