csaw

DOI: 10.18129/B9.bioc.csaw    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see csaw.

ChIP-Seq Analysis with Windows

Bioconductor version: 3.8

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

Author: Aaron Lun [aut, cre], Gordon Smyth [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF		csaw Vignette
PDF		csawUserGuide.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version	1.16.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	GPL-3
Depends	R (>= 3.5), GenomicRanges, SummarizedExperiment, BiocParallel
Imports	Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats
LinkingTo	Rhtslib(>= 1.13.1), zlibbioc, Rcpp
Suggests	org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat
SystemRequirements	C++11
Enhances
URL
Depends On Me	chipseqDB
Imports Me	diffHic, icetea, NADfinder, vulcan
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	csaw_1.16.1.tar.gz
Windows Binary	csaw_1.16.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	csaw_1.16.1.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	http://bioconductor.org/packages/csaw/
Package Downloads Report	Download Stats