Package: ChIPQC 1.43.0

Tom Carroll

ChIPQC: Quality metrics for ChIPseq data

Quality metrics for ChIPseq data.

Authors:Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark

ChIPQC_1.43.0.tar.gz
ChIPQC_1.43.0.zip(r-4.5)ChIPQC_1.43.0.zip(r-4.4)ChIPQC_1.43.0.zip(r-4.3)
ChIPQC_1.43.0.tgz(r-4.4-any)ChIPQC_1.43.0.tgz(r-4.3-any)
ChIPQC_1.43.0.tar.gz(r-4.5-noble)ChIPQC_1.43.0.tar.gz(r-4.4-noble)
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ChIPQC.pdf |ChIPQC.html✨
ChIPQC/json (API)
NEWS

# Install 'ChIPQC' in R:

install.packages('ChIPQC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

exampleExp - Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.
tamoxifen - Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.

On BioConductor:ChIPQC-1.43.0(bioc 3.21)ChIPQC-1.42.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing chipseq qualitycontrol reportwriting

5.44 score 137 scripts 592 downloads 15 mentions 40 exports 158 dependencies

Last updated 2 months agofrom:a673e8a16f. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	WARNING	Nov 29 2024
R-4.3-mac	WARNING	Oct 30 2024

Exports:averagepeaksignal ChIPQC ChIPQCreport ChIPQCsample coveragehistogram crosscoverage duplicateRate duplicates flagtagcounts fragmentlength FragmentLengthCrossCoverage frip mapped Normalisedaveragepeaksignal peaks plotCC plotCorHeatmap plotCoverageHist plotFribl plotFrip plotPeakProfile plotPrincomp plotRap plotRegi plotSSD QCannotation QCcontrol QCdba QCmetadata QCmetrics QCsample readlength ReadLengthCrossCoverage reads regi RelativeCrossCoverage ribl rip show ssd

Dependencies:abind amap AnnotationDbi apeglm ashr askpass base64enc bbmle bdsmatrix BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib cachem caTools chipseq cli coda codetools colorspace cpp11 crayon curl DBI DelayedArray deldir DESeq2 DiffBind digest dplyr emdbook etrunct evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel glue gplots GreyListChIP gtable gtools highr htmltools htmlwidgets httr hwriter interp invgamma IRanges irlba isoband jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice latticeExtra lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime mixsqp munsell mvtnorm nlme Nozzle.R1 numDeriv openssl pillar pkgconfig plogr plyr png pwalign R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppNumerical RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales ShortRead snow SparseArray SQUAREM statmod stringi stringr SummarizedExperiment sys systemPipeR tibble tidyselect tinytex truncnorm TxDb.Celegans.UCSC.ce6.ensGene TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Mmusculus.UCSC.mm9.knownGene TxDb.Rnorvegicus.UCSC.rn4.ensGene UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml zlibbioc

Assessing ChIP-seq sample quality with ChIPQC

Rendered fromChIPQC.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2020-07-17
Started: 2014-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ChIPQC - Quality metrics for ChIPseq data	ChIPQC-package
Retrieve average peak profiles	averagepeaksignal averagepeaksignal,ChIPQCexperiment-method averagepeaksignal,ChIPQCsample-method averagepeaksignal,list-method averagepeaksignal-methods
Construct a 'ChIPQCexperiment' object	ChIPQC
Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.	blacklist_hg19 exampleExp example_QCexperiment tamoxifen tamoxifen_QC
ChIPQCexperiment instances	ChIPQCexperiment ChIPQCexperiment-class show,ChIPQCexperiment-method
Generate a summary QC report	ChIPQCreport ChIPQCreport,ChIPQCexperiment-method ChIPQCreport,ChIPQCsample-method ChIPQCreport,list-method ChIPQCreport-methods
Class '"ChIPQCsample"'	ChIPQCsample ChIPQCsample-class show,ChIPQCsample-method
Retrieve histogram data representing densities of coverage pileups	coveragehistogram coveragehistogram,ChIPQCexperiment-method coveragehistogram,ChIPQCsample-method coveragehistogram,list-method coveragehistogram-methods
Retrieve the cross coverage values for a range of shift sizes	crosscoverage crosscoverage,ChIPQCexperiment-method crosscoverage,ChIPQCsample-method crosscoverage,list-method crosscoverage-methods
Retrieve duplication rates	duplicateRate duplicateRate,ChIPQCexperiment-method duplicateRate,ChIPQCsample-method duplicateRate,list-method duplicateRate-methods
Retrieve numbers of duplicate reads.	duplicates duplicates,ChIPQCexperiment-method duplicates,ChIPQCsample-method duplicates,list-method duplicates-methods
Retrieve numbers of reads that pass various filters	flagtagcounts flagtagcounts,ChIPQCexperiment-method flagtagcounts,ChIPQCsample-method flagtagcounts,list-method flagtagcounts-methods
Retrieve the estimated fragment length	fragmentlength fragmentlength,ChIPQCexperiment-method fragmentlength,ChIPQCsample-method fragmentlength,list-method fragmentlength-methods
Retrieve fraction of reads in peaks	frip frip,ChIPQCexperiment-method frip,ChIPQCsample-method frip,list-method frip-methods
Retrieve numbers of mapped reads	mapped mapped,ChIPQCexperiment-method mapped,ChIPQCsample-method mapped,list-method mapped-methods
Retrieve normalised average peak profiles	Normalisedaveragepeaksignal Normalisedaveragepeaksignal,ChIPQCexperiment-method Normalisedaveragepeaksignal,ChIPQCsample-method Normalisedaveragepeaksignal,list-method Normalisedaveragepeaksignal-methods
Retrieve peaks	peaks peaks,ChIPQCexperiment-method peaks,ChIPQCsample-method peaks,list-method peaks-methods
Generate Cross-Coverage plots	plotCC plotCC,ChIPQCexperiment-method plotCC,ChIPQCsample-method plotCC,list-method plotCC-methods
Generate Correlation Heatmap for ChIP samples	plotCorHeatmap plotCorHeatmap,ChIPQCexperiment-method plotCorHeatmap-methods
Generate coverage histogram plot	plotCoverageHist plotCoverageHist,ChIPQCexperiment-method plotCoverageHist,ChIPQCsample-method plotCoverageHist,list-method plotCoverageHist-methods
Generate fraction of reads in blacklist plot	plotFribl plotFribl,ChIPQCexperiment-method plotFribl,ChIPQCsample-method plotFribl,list-method plotFribl-methods
Generate fraction of reads in peaks plot	plotFrip plotFrip,ChIPQCexperiment-method plotFrip,ChIPQCsample-method plotFrip,list-method plotFrip-methods
Generate peak profile plots	plotPeakProfile plotPeakProfile,ChIPQCexperiment-method plotPeakProfile,ChIPQCsample-method plotPeakProfile,list-method plotPeakProfile-methods
Generate Principal Components Analysis plot for ChIP samples	plotPrincomp plotPrincomp,ChIPQCexperiment-method plotPrincomp-methods
Generate reads in peaks plot	plotRap plotRap,ChIPQCexperiment-method plotRap,ChIPQCsample-method plotRap,list-method plotRap-methods
Generate relative enrichment of genomic features plot	plotRegi plotRegi,ChIPQCexperiment-method plotRegi,ChIPQCsample-method plotRegi,list-method plotRegi-methods
Generate SSD plot	plotSSD plotSSD,ChIPQCexperiment-method plotSSD,ChIPQCsample-method plotSSD,list-method plotSSD-methods
Retrieve an annotation description, or a processed annotation	QCannotation QCannotation,ChIPQCexperiment-method QCannotation-methods
Retrieve control objects associated with a sample	QCcontrol QCcontrol,ChIPQCexperiment-method QCcontrol-methods
Retrieve the 'DBA-object' object associated with an experiment	QCdba QCdba,ChIPQCexperiment-method QCdba-methods
Retrieve metadata associated with an experiment	QCmetadata QCmetadata,ChIPQCexperiment-method QCmetadata,list-method QCmetadata-methods
Retrieve consolidated set of QC metrics	QCmetrics QCmetrics,ChIPQCexperiment-method QCmetrics,ChIPQCsample-method QCmetrics,list-method QCmetrics-methods
Retrieve sample objects associated with an experiment	QCsample QCsample,ChIPQCexperiment-method QCsample-methods
Retrieve read length values	readlength readlength,ChIPQCexperiment-method readlength,ChIPQCsample-method readlength,list-method readlength-methods
Retrieve the cross coverage values when extending reads to the optimal fragment length.	FragmentLengthCrossCoverage FragmentLengthCrossCoverage,ChIPQCexperiment-method FragmentLengthCrossCoverage,ChIPQCsample-method FragmentLengthCrossCoverage,list-method FragmentLengthCrossCoverage-methods
Retrieve the cross coverage values without extending reads	ReadLengthCrossCoverage ReadLengthCrossCoverage,ChIPQCexperiment-method ReadLengthCrossCoverage,ChIPQCsample-method ReadLengthCrossCoverage,list-method ReadLengthCrossCoverage-methods
Retrieve numbers of reads	reads reads,ChIPQCexperiment-method reads,ChIPQCsample-method reads,list-method reads-methods
Retrieve genomic profile information	regi regi,ChIPQCexperiment-method regi,ChIPQCsample-method regi,list-method regi-methods
Retrieve the relative cross coverage values for a range of shift sizes	RelativeCrossCoverage RelativeCrossCoverage,ChIPQCexperiment-method RelativeCrossCoverage,ChIPQCsample-method RelativeCrossCoverage,list-method RelativeCrossCoverage-methods
Retrieve numbers of reads overlapping blacklisted regions	ribl ribl,ChIPQCexperiment-method ribl,ChIPQCsample-method ribl,list-method ribl-methods
Retrieve numbers of reads overlapping peaks	rip rip,ChIPQCexperiment-method rip,ChIPQCsample-method rip,list-method rip-methods
Retrieve SSD (squared sum of deviations) values of peak coverage	ssd ssd,ChIPQCexperiment-method ssd,ChIPQCsample-method ssd,list-method ssd-methods