csaw

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

ChIP-Seq Analysis with Windows

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DOI: 10.18129/B9.bioc.csaw

Bioconductor version: Development (3.23)

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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 1.45.0

In Bioconductor since BioC 3.0 (R-3.1) (11 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, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager

Linking To Rhtslib, Rcpp

Enhances

Depends On Me csawBook

Imports Me diffHic, epigraHMM, extraChIPs, icetea, mutscan, NADfinder, hicream, treediff

Suggests Me 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_1.45.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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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