csaw

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

ChIP-Seq Analysis with Windows

Bioconductor version: Development (3.24)

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>

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

Aaron Lun, Gordon Smyth. csaw: ChIP-Seq Analysis with Windows. doi:10.18129/B9.bioc.csaw, R package version 1.47.1, https://bioconductor.org/packages/csaw.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

Introduction	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version	1.47.1
In Bioconductor since	BioC 3.0 (R-3.1) (12 years)
License	GPL-3
Depends	R (>= 3.5.0), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1)
Imports	Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod, utils
System Requirements	C++11, GNU make
URL

Suggests	AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, cigarillo, knitr, BiocStyle, rmarkdown, BiocManager
Linking To	Rhtslib, Rcpp
Enhances
Depends On Me	csawBook
Imports Me	diffHic, epigraHMM, extraChIPs, hicream, icetea, mutscan, NADfinder, treediff, vulcan
Suggests Me	chipseqDB, DiffBind, GRaNIE
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	csaw_1.47.1.tar.gz
Windows Binary (x86_64)	csaw_1.47.1.zip
macOS Binary (big-sur-x86_64)	csaw_1.47.1.tgz
macOS Binary (sonoma-arm64)	csaw_1.47.1.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