To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPQC")

In most cases, you don't need to download the package archive at all.

ChIPQC

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see ChIPQC.

Quality metrics for ChIPseq data

Bioconductor version: 3.2

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPQC")

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 1.6.1
In Bioconductor since BioC 2.14 (R-3.1) (2 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
LinkingTo
Suggests BiocStyle, 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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source ChIPQC_1.6.1.tar.gz
Windows Binary ChIPQC_1.6.1.zip
Mac OS X 10.6 (Snow Leopard) ChIPQC_1.6.1.tgz
Mac OS X 10.9 (Mavericks) ChIPQC_1.6.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChIPQC/tree/release-3.2
Package Short Url http://bioconductor.org/packages/ChIPQC/
Package Downloads Report Download Stats

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