To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ChIPQC")

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

ChIPQC

Quality metrics for ChIPseq data

Bioconductor version: Release (3.0)

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:

source("http://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 1.2.0
In Bioconductor since BioC 2.14 (R-3.1)
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
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
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source ChIPQC_1.2.0.tar.gz
Windows Binary ChIPQC_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChIPQC_1.2.0.tgz
Mac OS X 10.9 (Mavericks) ChIPQC_1.2.0.tgz
Browse/checkout source (username/password: readonly)
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