DOI: 10.18129/B9.bioc.csaw  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see csaw.

ChIP-Seq Analysis with Windows

Bioconductor version: 3.17

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")):


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biocViews Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.34.0
In Bioconductor since BioC 3.0 (R-3.1) (9 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
LinkingTo Rhtslib, zlibbioc, Rcpp
Suggests AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
SystemRequirements C++11, GNU make
Depends On Me csawBook
Imports Me diffHic, epigraHMM, extraChIPs, icetea, NADfinder, vulcan
Suggests Me chipseqDB, DiffBind, GRaNIE
Links To Me
Build Report  

Package Archives

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Source Package csaw_1.34.0.tar.gz
Windows Binary csaw_1.34.0.zip (64-bit only)
macOS Binary (x86_64) csaw_1.34.0.tgz
macOS Binary (arm64) csaw_1.33.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/csaw
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/csaw
Bioc Package Browser https://code.bioconductor.org/browse/csaw/
Package Short Url https://bioconductor.org/packages/csaw/
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