csaw

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see csaw.

ChIP-Seq Analysis with Windows


Bioconductor version: 3.12

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 "4.0") 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 1.24.3
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends GenomicRanges, SummarizedExperiment
Imports Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, utils
System Requirements C++11, GNU make
URL
See More
Suggests org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
Linking To Rhtslib, zlibbioc, Rcpp
Enhances
Depends On Me
Imports Me diffHic, icetea, NADfinder, vulcan
Suggests Me chipseqDB, csawUsersGuide, tximport
Links To Me
Build Report Build Report

Package Archives

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

Source Package csaw_1.24.3.tar.gz
Windows Binary csaw_1.24.3.zip (32- & 64-bit)
macOS 10.13 (High Sierra) csaw_1.24.3.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
Old Source Packages for BioC 3.12 Source Archive