csaw

DOI: 10.18129/B9.bioc.csaw  

ChIP-Seq Analysis with Windows

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Introduction
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version	1.32.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 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
LinkingTo	Rhtslib, zlibbioc, Rcpp
Suggests	AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
SystemRequirements	C++11, GNU make
Enhances
URL
Depends On Me	csawBook
Imports Me	diffHic, epigraHMM, extraChIPs, icetea, NADfinder, vulcan
Suggests Me	chipseqDB, GRaNIE
Links To Me
Build Report

Package Archives

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

Source Package	csaw_1.32.0.tar.gz
Windows Binary	csaw_1.32.0.zip (64-bit only)
macOS Binary (x86_64)	csaw_1.32.0.tgz
macOS Binary (arm64)	csaw_1.32.0.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