csaw

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see csaw.

ChIP-Seq Analysis with Windows


Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("csaw")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

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

Details

biocViews Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.14.1
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges, SummarizedExperiment, BiocParallel
Imports Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, Rhtslib, stats, Rcpp
System Requirements C++11
URL
See More
Suggests org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene
Linking To Rhtslib(>= 1.12.1), zlibbioc, Rcpp
Enhances
Depends On Me chipseqDB
Imports Me diffHic, NADfinder, vulcan
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package csaw_1.14.1.tar.gz
Windows Binary csaw_1.14.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) csaw_1.14.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/csaw
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/csaw
Package Short Url https://bioconductor.org/packages/csaw/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive