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 1.2.2
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
SystemRequirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source ChIPQC_1.2.2.tar.gz
Windows Binary ChIPQC_1.2.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChIPQC_1.2.2.tgz
Mac OS X 10.9 (Mavericks) ChIPQC_1.2.2.tgz
Browse/checkout source (username/password: readonly)
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