ChIPQC

This is the released version of ChIPQC; for the devel version, see ChIPQC.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

Quality metrics for ChIPseq data

Bioconductor version: Release (3.23)

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 <bioconductor at starkhome.com>

Citation (from within R, enter citation("ChIPQC")):

Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark. ChIPQC: Quality metrics for ChIPseq data. doi:10.18129/B9.bioc.ChIPQC, R package version 1.48.3, https://bioconductor.org/packages/ChIPQC.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, QualityControl, ReportWriting, Sequencing, Software
Version	1.48.3
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	GPL (>= 3)
Depends	R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19), BiocParallel
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, methods, reshape2, 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
System Requirements
URL

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Build Report	Build Report, r-universe

Package Archives

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

Source Package	ChIPQC_1.48.3.tar.gz
Windows Binary (x86_64)	ChIPQC_1.48.3.zip
macOS Binary (big-sur-x86_64)	ChIPQC_1.48.3.tgz
macOS Binary (sonoma-arm64)	ChIPQC_1.48.3.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
Old Source Packages for BioC 3.23	Source Archive