ChIPQC: Quality metrics for ChIPseq data

Quality metrics for ChIPseq data.

Author
Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark
Date of publication
None
Maintainer
Tom Carroll <tc.infomatics@gmail.com>, Rory Stark <rory.stark@cruk.cam.ac.uk>
License
GPL (>= 3)
Version
1.10.2

View on Bioconductor

Man pages

averagepeaksignal-methods
Retrieve average peak profiles
ChIPQC
Construct a 'ChIPQCexperiment' object
ChIPQC-data
Example data sets for 'ChIPQC' package, each containing a...
ChIPQCexperiment-class
ChIPQCexperiment instances
ChIPQC-package
ChIPQC - Quality metrics for ChIPseq data
ChIPQCreport
Generate a summary QC report
ChIPQCsample-class
Class '"ChIPQCsample"'
coveragehistogram-methods
Retrieve histogram data representing densities of coverage...
crosscoverage-methods
Retrieve the cross coverage values for a range of shift sizes
duplicateRate-methods
Retrieve duplication rates
duplicates-methods
Retrieve numbers of duplicate reads.
flagtagcounts-methods
Retrieve numbers of reads that pass various filters
FragmentLengthCrossCoverage-methods
Retrieve the cross coverage values when extending reads to...
fragmentlength-methods
Retrieve the estimated fragment length
frip-methods
Retrieve fraction of reads in peaks
mapped-methods
Retrieve numbers of mapped reads
Normalisedaveragepeaksignal-methods
Retrieve normalised average peak profiles
peaks-methods
Retrieve peaks
plotCC-methods
Generate Cross-Coverage plots
plotCorHeatmap-methods
Generate Correlation Heatmap for ChIP samples
plotCoverageHist-methods
Generate coverage histogram plot
plotFribl-methods
Generate fraction of reads in blacklist plot
plotFrip-methods
Generate fraction of reads in peaks plot
plotPeakProfile-methods
Generate peak profile plots
plotPrincomp-methods
Generate Principal Components Analysis plot for ChIP samples
plotRap-methods
Generate reads in peaks plot
plotRegi-methods
Generate relative enrichment of genomic features plot
plotSSD-methods
Generate SSD plot
QCannotation-methods
Retrieve an annotation description, or a processed annotation
QCcontrol-methods
Retrieve control objects associated with a sample
QCdba-methods
Retrieve the 'DBA' object associated with an experiment
QCmetadata-methods
Retrieve metadata associated with an experiment
QCmetrics-methods
Retrieve consolidated set of QC metrics
QCsample-methods
Retrieve sample objects associated with an experiment
ReadLengthCrossCoverage-methods
Retrieve the cross coverage values without extending reads
readlength-methods
Retrieve read length values
reads-methods
Retrieve numbers of reads
regi-methods
Retrieve genomic profile information
RelativeCrossCoverage-methods
Retrieve the relative cross coverage values for a range of...
ribl-methods
Retrieve numbers of reads overlapping blacklisted regions
rip-methods
Retrieve numbers of reads overlapping peaks
ssd-methods
Retrieve SSD (squared sum of deviations) values of peak...

Files in this package

ChIPQC/ChIPQC.Rproj
ChIPQC/DESCRIPTION
ChIPQC/NAMESPACE
ChIPQC/R
ChIPQC/R/ChIPQC_IF.R
ChIPQC/R/ChIPQCexperiment-class.R
ChIPQC/R/ChIPQCsample-class.R
ChIPQC/R/dbaplots.R
ChIPQC/R/plots.r
ChIPQC/R/report.r
ChIPQC/R/sampleQC.R
ChIPQC/R/utilities.R
ChIPQC/build
ChIPQC/build/vignette.rds
ChIPQC/data
ChIPQC/data/blacklist_hg19.RData
ChIPQC/data/datalist
ChIPQC/data/example_QCexperiment.RData
ChIPQC/data/tamoxifen_QC.RData
ChIPQC/inst
ChIPQC/inst/CITATION
ChIPQC/inst/NEWS.Rd
ChIPQC/inst/doc
ChIPQC/inst/doc/ChIPQC.R
ChIPQC/inst/doc/ChIPQC.Rnw
ChIPQC/inst/doc/ChIPQC.pdf
ChIPQC/inst/doc/ChIPQCSampleReport.pdf
ChIPQC/inst/doc/index.html
ChIPQC/inst/extdata
ChIPQC/inst/extdata/blacklist_hg19.bed
ChIPQC/inst/extdata/example_QCexperiment.csv
ChIPQC/inst/extdata/tamoxifenQC.csv
ChIPQC/man
ChIPQC/man/ChIPQC-data.Rd
ChIPQC/man/ChIPQC-package.Rd
ChIPQC/man/ChIPQC.Rd
ChIPQC/man/ChIPQCexperiment-class.Rd
ChIPQC/man/ChIPQCreport.Rd
ChIPQC/man/ChIPQCsample-class.Rd
ChIPQC/man/FragmentLengthCrossCoverage-methods.Rd
ChIPQC/man/Normalisedaveragepeaksignal-methods.Rd
ChIPQC/man/QCannotation-methods.Rd
ChIPQC/man/QCcontrol-methods.Rd
ChIPQC/man/QCdba-methods.Rd
ChIPQC/man/QCmetadata-methods.Rd
ChIPQC/man/QCmetrics-methods.Rd
ChIPQC/man/QCsample-methods.Rd
ChIPQC/man/ReadLengthCrossCoverage-methods.Rd
ChIPQC/man/RelativeCrossCoverage-methods.Rd
ChIPQC/man/averagepeaksignal-methods.Rd
ChIPQC/man/coveragehistogram-methods.Rd
ChIPQC/man/crosscoverage-methods.Rd
ChIPQC/man/duplicateRate-methods.Rd
ChIPQC/man/duplicates-methods.Rd
ChIPQC/man/flagtagcounts-methods.Rd
ChIPQC/man/fragmentlength-methods.Rd
ChIPQC/man/frip-methods.Rd
ChIPQC/man/mapped-methods.Rd
ChIPQC/man/peaks-methods.Rd
ChIPQC/man/plotCC-methods.Rd
ChIPQC/man/plotCorHeatmap-methods.Rd
ChIPQC/man/plotCoverageHist-methods.Rd
ChIPQC/man/plotFribl-methods.Rd
ChIPQC/man/plotFrip-methods.Rd
ChIPQC/man/plotPeakProfile-methods.Rd
ChIPQC/man/plotPrincomp-methods.Rd
ChIPQC/man/plotRap-methods.Rd
ChIPQC/man/plotRegi-methods.Rd
ChIPQC/man/plotSSD-methods.Rd
ChIPQC/man/readlength-methods.Rd
ChIPQC/man/reads-methods.Rd
ChIPQC/man/regi-methods.Rd
ChIPQC/man/ribl-methods.Rd
ChIPQC/man/rip-methods.Rd
ChIPQC/man/ssd-methods.Rd
ChIPQC/vignettes
ChIPQC/vignettes/ChIPQC.Rnw
ChIPQC/vignettes/ChIPQC.bib