Registration Open for Bioc2024 July 24-26


ChIP-Seq Analysis with Windows

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

Introduction HTML R Script
Reference Manual PDF


biocViews Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License GPL-3
Depends R (>= 3.5.0), GenomicRanges, SummarizedExperiment
Imports Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils
System Requirements C++11, GNU make
See More
Suggests AnnotationDbi,, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
Linking To Rhtslib, zlibbioc, Rcpp
Depends On Me csawBook
Imports Me diffHic, epigraHMM, extraChIPs, icetea, NADfinder, vulcan, treediff
Suggests Me DiffBind, GRaNIE, chipseqDB
Links To Me
Build Report Build Report

Package Archives

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

Source Package csaw_1.38.0.tar.gz
Windows Binary
macOS Binary (x86_64) csaw_1.38.0.tgz
macOS Binary (arm64) csaw_1.38.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats