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ChIPQC

This is the development version of ChIPQC; for the stable release version, see ChIPQC.

Quality metrics for ChIPseq data

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews ChIPSeq, QualityControl, ReportWriting, Sequencing, Software
Version 1.37.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 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, 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_1.37.0.tar.gz
Windows Binary ChIPQC_1.37.0.zip
macOS Binary (x86_64) ChIPQC_1.37.0.tgz
macOS Binary (arm64)
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