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.
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ChIPQC.
Bioconductor version: 3.3
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("ChIPQC")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPQC")
R Script | Assessing ChIP-seq sample quality with ChIPQC | |
ChIPQCSampleReport.pdf | ||
Reference Manual | ||
Text | NEWS |
biocViews | ChIPSeq, QualityControl, ReportWriting, Sequencing, Software |
Version | 1.8.9 |
In Bioconductor since | BioC 2.14 (R-3.1) (2.5 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.hg38.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 |
LinkingTo | |
Suggests | BiocStyle |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | ChIPQC_1.8.9.tar.gz |
Windows Binary | ChIPQC_1.8.9.zip |
Mac OS X 10.9 (Mavericks) | ChIPQC_1.8.9.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/ChIPQC/tree/release-3.3 |
Package Short Url | http://bioconductor.org/packages/ChIPQC/ |
Package Downloads Report | Download Stats |
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