ChIPQC
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ChIPQC.
Quality metrics for ChIPseq data
Bioconductor version: 3.9
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 "3.6") 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 | 1.20.0 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPQC_1.20.0.tar.gz |
| Windows Binary | ChIPQC_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | ChIPQC_1.20.0.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 3.9 | Source Archive |