Bioconductor release scheduled for October 29

ChIPQC

This is the development version of ChIPQC; for the stable release version, see ChIPQC.

Quality metrics for ChIPseq data


Bioconductor version: Development (3.22)

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 <bioconductor at starkhome.com>

Citation (from within R, enter citation("ChIPQC")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ChIPQC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews ChIPSeq, QualityControl, ReportWriting, Sequencing, Software
Version 1.45.0
In Bioconductor since BioC 2.14 (R-3.1) (11.5 years)
License GPL (>= 3)
Depends R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges(>= 1.17.19), BiocParallel
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, 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
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Package Archives

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

Source Package
Windows Binary (x86_64) ChIPQC_1.45.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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