ChIPQC

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ChIPQC.

Quality metrics for ChIPseq data


Bioconductor version: 3.7

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 "3.5") 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

Details

biocViews ChIPSeq, QualityControl, ReportWriting, Sequencing, Software
Version 1.16.1
In Bioconductor since BioC 2.14 (R-3.1) (10 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
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Package Archives

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

Source Package ChIPQC_1.16.1.tar.gz
Windows Binary ChIPQC_1.16.1.zip
Mac OS X 10.11 (El Capitan) ChIPQC_1.16.1.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 3.7 Source Archive