ChIPQC

DOI: 10.18129/B9.bioc.ChIPQC    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ChIPQC.

Quality metrics for ChIPseq data

Bioconductor version: 3.12

Quality metrics for ChIPseq data.

Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark

Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark at cruk.cam.ac.uk>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("ChIPQC")

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("ChIPQC")

 

PDF	R Script	Assessing ChIP-seq sample quality with ChIPQC
PDF		ChIPQCSampleReport.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, QualityControl, ReportWriting, Sequencing, Software
Version	1.26.0
In Bioconductor since	BioC 2.14 (R-3.1) (7 years)
License	GPL (>= 3)
Depends	R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges(>= 1.17.19)
Imports	BiocGenerics(>= 0.11.3), S4Vectors(>= 0.1.0), IRanges(>= 1.99.17), Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.16), chipseq(>= 1.12.0), gtools, BiocParallel, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene
LinkingTo
Suggests	BiocStyle
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Depends On Me
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Build Report

Package Archives

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

Source Package	ChIPQC_1.26.0.tar.gz
Windows Binary	ChIPQC_1.26.0.zip
macOS 10.13 (High Sierra)	ChIPQC_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChIPQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPQC
Package Short Url	https://bioconductor.org/packages/ChIPQC/
Package Downloads Report	Download Stats