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ChIPQC

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ChIPQC.

Quality metrics for ChIPseq data


Bioconductor version: 3.16

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>

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

Installation

To install this package, start R (version "4.2") 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 1.34.1
In Bioconductor since BioC 2.14 (R-3.1) (10 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, 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
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Package Archives

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

Source Package ChIPQC_1.34.1.tar.gz
Windows Binary ChIPQC_1.34.1.zip
macOS Binary (x86_64) ChIPQC_1.34.1.tgz
macOS Binary (arm64) ChIPQC_1.34.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChIPQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIPQC
Bioc Package Browser https://code.bioconductor.org/browse/ChIPQC/
Package Short Url https://bioconductor.org/packages/ChIPQC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive