CoverageView: Coverage visualization package for R

Share:

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

Author
Ernesto Lowy
Date of publication
None
Maintainer
Ernesto Lowy <ernestolowy@gmail.com>
License
Artistic-2.0
Version
1.10.0

View on Bioconductor

Man pages

CoverageBamFile-class
Class '"CoverageBamFile"'
CoverageBigWigFile-class
Class '"CoverageBigWigFile"'
CoverageView-internal
Internal Methods
CoverageView-package
Coverage visualization package for R
cov.interval
arithmetic operation on an interval
cov.matrix
Compute a coverage matrix
DF_H3K36me3
Example of a coverage matrix using the ChIP-seq data for the...
DF_H3K36me3_control
Example of a coverage matrix using the control replicate for...
DF_H3K4me3
Example of a coverage matrix using the ChIP-seq data for the...
DF_H3K4me3_ctl
Example of a coverage matrix using the control replicate for...
DF_H3K4me3_nopeaks_ratios
Example of a matrix with the ratio of the coverages using the...
draw.heatmap
Draw a coverage heatmap
draw.profile
Draw a coverage profile
export.wig
Generates a WIG file containing the coverage values for a...
FoxA1_chr19
Example of a coverage matrix using the ChIP-seq data for the...
genome.covplot.cumdepth
Generates a cumulative genome coverage plot
genome.covplot.depth
Generates a genome coverage plot
write.profile
Write coverage values into a file

Files in this package

CoverageView/.BBSoptions
CoverageView/.Rinstignore
CoverageView/DESCRIPTION
CoverageView/NAMESPACE
CoverageView/R
CoverageView/R/AllClasses.R
CoverageView/R/AllGenerics.R
CoverageView/R/coord.to.granges.R
CoverageView/R/cov.bin.R
CoverageView/R/cov.interval.R
CoverageView/R/cov.matrix.R
CoverageView/R/do.normalization.R
CoverageView/R/draw.heatmap.R
CoverageView/R/draw.profile.R
CoverageView/R/export.wig.R
CoverageView/R/genome.covplot.R
CoverageView/R/imageScale.R
CoverageView/R/methods-CoverageBamFile.R
CoverageView/R/methods-CoverageBigWigFile.R
CoverageView/R/write.profile.R
CoverageView/build
CoverageView/build/vignette.rds
CoverageView/data
CoverageView/data/DF_H3K36me3.RData
CoverageView/data/DF_H3K36me3_control.RData
CoverageView/data/DF_H3K4me3.RData
CoverageView/data/DF_H3K4me3_ctl.RData
CoverageView/data/DF_H3K4me3_nopeaks_ratios.RData
CoverageView/data/FoxA1_chr19.RData
CoverageView/data/datalist
CoverageView/inst
CoverageView/inst/doc
CoverageView/inst/doc/CoverageView.R
CoverageView/inst/doc/CoverageView.Rnw
CoverageView/inst/doc/CoverageView.pdf
CoverageView/inst/extdata
CoverageView/inst/extdata/FoxA1.chr19.bed
CoverageView/inst/extdata/H3K4me3.chr19.bed
CoverageView/inst/extdata/H3K4me3.chr19.nopeaks.bed
CoverageView/inst/extdata/ctrl.bam
CoverageView/inst/extdata/ctrl.bam.bai
CoverageView/inst/extdata/ctrl.bw
CoverageView/inst/extdata/test.gff
CoverageView/inst/extdata/testTSS.bed
CoverageView/inst/extdata/treat.bam
CoverageView/inst/extdata/treat.bam.bai
CoverageView/inst/extdata/treat.bw
CoverageView/man
CoverageView/man/CoverageBamFile-class.Rd
CoverageView/man/CoverageBigWigFile-class.Rd
CoverageView/man/CoverageView-internal.Rd
CoverageView/man/CoverageView-package.Rd
CoverageView/man/DF_H3K36me3.Rd
CoverageView/man/DF_H3K36me3_control.Rd
CoverageView/man/DF_H3K4me3.Rd
CoverageView/man/DF_H3K4me3_ctl.Rd
CoverageView/man/DF_H3K4me3_nopeaks_ratios.Rd
CoverageView/man/FoxA1_chr19.Rd
CoverageView/man/cov.interval.Rd
CoverageView/man/cov.matrix.Rd
CoverageView/man/draw.heatmap.Rd
CoverageView/man/draw.profile.Rd
CoverageView/man/export.wig.Rd
CoverageView/man/genome.covplot.cumdepth.Rd
CoverageView/man/genome.covplot.depth.Rd
CoverageView/man/write.profile.Rd
CoverageView/vignettes
CoverageView/vignettes/CoverageView.Rnw
CoverageView/vignettes/references.bib