Package: CoverageView 1.51.1

Ernesto Lowy

CoverageView: Coverage visualization package for R

This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome

Authors:Ernesto Lowy

CoverageView_1.51.1.tar.gz
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CoverageView_1.51.1.tgz(r-4.6-any)CoverageView_1.51.1.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
CoverageView/json (API)

# Install 'CoverageView' in R:
install.packages('CoverageView', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • DF_H3K36me3 - Example of a coverage matrix using the ChIP-seq data for the H3K36me3 histone modification experiment
  • DF_H3K36me3_control - Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K36me3 histone modification experiment
  • DF_H3K4me3 - Example of a coverage matrix using the ChIP-seq data for the H3K4me3 histone modification experiment
  • DF_H3K4me3_ctl - Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K4me3 histone modification experiment
  • DF_H3K4me3_nopeaks_ratios - Example of a matrix with the ratio of the coverages using the ChIP-seq data for the H3K4me3 histone modification experiment
  • FoxA1_chr19 - Example of a coverage matrix using the ChIP-seq data for the FoxA1 transcription factor experiment

On BioConductor:CoverageView-1.51.0(bioc 3.24)CoverageView-1.50.0(bioc 3.23)

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

immunooncologyvisualizationrnaseqchipseqsequencingtechnologysoftware

2.95 score 7 scripts 502 downloads 3 mentions 12 exports 49 dependencies

Last updated from:17f9e533f6. Checks:5 ERROR, 4 WARNING, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR177
linux-devel-x86_64WARNING323
source / vignettesERROR244
linux-release-x86_64WARNING321
macos-release-arm64WARNING232
macos-oldrel-arm64WARNING200
windows-develERROR310
windows-releaseERROR250
windows-oldrelERROR245
wasm-releaseOK135

Exports:cov.bincov.intervalcov.matrixCoverageBamFileCoverageBigWigFiledraw.heatmapdraw.profileexport.wiggenome.covplot.cumdepthgenome.covplot.depthimageScalewrite.profile

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarillocodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Coverage visualization package for RCoverageView-package CoverageView
arithmetic operation on an intervalcov.interval cov.interval,CoverageBamFile,CoverageBamFile-method cov.interval,CoverageBamFile-method cov.interval,CoverageBigWigFile,CoverageBigWigFile-method cov.interval,CoverageBigWigFile-method
Compute a coverage matrixcov.matrix cov.matrix,ANY,ANY-method cov.matrix,ANY,missing-method
Class '"CoverageBamFile"'CoverageBamFile CoverageBamFile-class path,CoverageBamFile-method reads_mapped,CoverageBamFile-method run_type,CoverageBamFile-method show,CoverageBamFile-method
Class '"CoverageBigWigFile"'CoverageBigWigFile CoverageBigWigFile-class show,CoverageBigWigFile-method
Example of a coverage matrix using the ChIP-seq data for the H3K36me3 histone modification experimentDF_H3K36me3
Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K36me3 histone modification experimentDF_H3K36me3_control
Example of a coverage matrix using the ChIP-seq data for the H3K4me3 histone modification experimentDF_H3K4me3
Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K4me3 histone modification experimentDF_H3K4me3_ctl
Example of a matrix with the ratio of the coverages using the ChIP-seq data for the H3K4me3 histone modification experimentDF_H3K4me3_nopeaks_ratios
Draw a coverage heatmapdraw.heatmap draw.heatmap,list-method draw.heatmap,matrix-method
Draw a coverage profiledraw.profile draw.profile,list-method draw.profile,matrix-method
Generates a WIG file containing the coverage values for a certain genomic intervalexport.wig export.wig,numeric-method
Example of a coverage matrix using the ChIP-seq data for the FoxA1 transcription factor experimentFoxA1_chr19
Generates a cumulative genome coverage plotgenome.covplot.cumdepth genome.covplot.cumdepth,CoverageBamFile-method genome.covplot.cumdepth,list-method
Generates a genome coverage plotgenome.covplot.depth genome.covplot.depth,CoverageBamFile-method genome.covplot.depth,list-method
Write coverage values into a filewrite.profile write.profile,matrix-method