Package: CoverageView 1.45.0

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

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CoverageView.pdf |CoverageView.html✨
CoverageView/json (API)

# Install 'CoverageView' in R:
install.packages('CoverageView', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.45.0(bioc 3.21)CoverageView-1.44.0(bioc 3.20)

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

immunooncologyvisualizationrnaseqchipseqsequencingtechnologysoftware

2.78 score 5 scripts 296 downloads 3 mentions 12 exports 50 dependencies

Last updated 23 days agofrom:b74ea21b99. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

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

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

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