Bioconductor – ChIPQC

 
 

This package is for version 3.1 of Bioconductor;
for the stable, up-to-date release version, see
ChIPQC.

Quality metrics for ChIPseq data

Bioconductor version: 3.1

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 1.4.4
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
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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, TxDb.Hsapiens.UCSC.hg38.knownGene
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