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csaw

ChIP-Seq Analysis with Windows

Bioconductor version: Release (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")):

Installation

To install this package, start R (version "4.3") 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")
Introduction HTML R Script
Reference Manual PDF
NEWS Text

Details

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
Linking To Rhtslib, zlibbioc, Rcpp
Suggests AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
System Requirements C++11, GNU make
Enhances
URL
See More
Depends On Me csawBook
Imports Me diffHic, epigraHMM, extraChIPs, icetea, NADfinder, vulcan
Suggests Me chipseqDB, DiffBind, GRaNIE
Links To Me
Build Report  

Package Archives

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

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/
Package Downloads Report Download Stats