ChIPQC
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ChIPQC.
Quality metrics for ChIPseq data
Bioconductor version: 3.13
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 (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChIPQC")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPQC")
Assessing ChIP-seq sample quality with ChIPQC | R Script | |
ChIPQCSampleReport.pdf | ||
Reference Manual | ||
NEWS | Text |
Details
biocViews | ChIPSeq, QualityControl, ReportWriting, Sequencing, Software |
Version | 1.28.0 |
In Bioconductor since | BioC 2.14 (R-3.1) (10 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.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 |
See More
Suggests | BiocStyle |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | ChIPQC_1.28.0.tar.gz |
Windows Binary | ChIPQC_1.28.0.zip |
macOS 10.13 (High Sierra) | ChIPQC_1.28.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/ChIPQC |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPQC |
Bioc Package Browser | https://code.bioconductor.org/browse/ChIPQC/ |
Package Short Url | https://bioconductor.org/packages/ChIPQC/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.13 | Source Archive |