csaw

DOI: 10.18129/B9.bioc.csaw    

ChIP-Seq Analysis with Windows

Bioconductor version: Release (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("csaw", version = "3.8")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("csaw")

 

PDF csaw Vignette
PDF csawUserGuide.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges, SummarizedExperiment, BiocParallel
Imports Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats
LinkingTo Rhtslib(>= 1.13.1), zlibbioc, Rcpp
Suggests org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat
SystemRequirements C++11
Enhances
URL
Depends On Me chipseqDB
Imports Me diffHic, icetea, NADfinder, vulcan
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package csaw_1.16.0.tar.gz
Windows Binary csaw_1.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) csaw_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/csaw
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/csaw
Package Short Url http://bioconductor.org/packages/csaw/
Package Downloads Report Download Stats

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