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ChIPQC

This is the released version of ChIPQC; for the devel version, see ChIPQC.

Quality metrics for ChIPseq data

Bioconductor version: Release (3.21)

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")

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 PDF R Script ChIPQCSampleReport.pdf PDF Reference Manual PDF NEWS Text Details biocViews ChIPSeq, QualityControl, ReportWriting, Sequencing, Software Version 1.44.0 In Bioconductor since BioC 2.14 (R-3.1) (11 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 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.

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