chipseq

DOI: 10.18129/B9.bioc.chipseq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see chipseq.

chipseq: A package for analyzing chipseq data

Bioconductor version: 3.9

Tools for helping process short read data for chipseq experiments

Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("chipseq")

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("chipseq")

 

PDF	R Script	A Sample ChIP-Seq analysis workflow
PDF		Reference Manual

Details

biocViews	ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software
Version	1.34.0
In Bioconductor since	BioC 2.5 (R-2.10) (10 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), ShortRead
Imports	methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead
LinkingTo
Suggests	BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene
SystemRequirements
Enhances
URL
Depends On Me	PING
Imports Me	ChIPQC, CopywriteR, HTSeqGenie, soGGi, transcriptR
Suggests Me	GenoGAM, ggbio
Links To Me
Build Report

Package Archives

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

Source Package	chipseq_1.34.0.tar.gz
Windows Binary	chipseq_1.34.0.zip
Mac OS X 10.11 (El Capitan)	chipseq_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/chipseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/chipseq
Package Short Url	https://bioconductor.org/packages/chipseq/
Package Downloads Report	Download Stats