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Bioconductor - csaw (development version)

csaw

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

ChIP-Seq Analysis with Windows

Bioconductor version: Development (3.22)

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 "4.5") 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")
Details biocViews Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software Version 1.43.1 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 See More 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, 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.

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