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

AuthorErnesto Lowy
Date of publicationNone
MaintainerErnesto Lowy <ernestolowy@gmail.com>
LicenseArtistic-2.0
Version1.10.0

View on Bioconductor

Functions

.bed.to.GRanges Man page
.cov.bin Man page
cov.bin Man page
cov.bin,ANY,missing,numeric,GRanges,missing-method Man page
cov.bin,ANY,missing,numeric,missing,CoverageBamFile,missing-meth Man page
cov.bin,ANY,missing,numeric,missing,CoverageBigWigFile,missing-m Man page
cov.bin,ANY,missing,numeric,missing,missing-method Man page
cov.bin,ANY,numeric,missing,GRanges,missing-method Man page
cov.bin,ANY,numeric,missing,missing,CoverageBamFile,missing-meth Man page
cov.bin,ANY,numeric,missing,missing,CoverageBigWigFile,missing-m Man page
cov.bin,ANY,numeric,missing,missing,missing-method Man page
cov.bin-methods Man page
cov.bin,missing,missing,missing,GRanges,character-method Man page
cov.bin,missing,missing,missing,GRanges,missing,character-method Man page
cov.bin,missing,missing,missing,missing,character-method Man page
cov.bin,missing,missing,missing,missing,CoverageBamFile,characte Man page
CoverageBamFile Man page
CoverageBamFile-class Man page
CoverageBigWigFile Man page
CoverageBigWigFile-class Man page
CoverageView Man page
CoverageView-internal Man page
CoverageView-package Man page
cov.interval Man page
cov.interval,CoverageBamFile,CoverageBamFile-method Man page
cov.interval,CoverageBamFile-method Man page
cov.interval,CoverageBigWigFile,CoverageBigWigFile-method Man page
cov.interval,CoverageBigWigFile-method Man page
cov.matrix Man page
cov.matrix,ANY,ANY-method Man page
cov.matrix,ANY,missing-method Man page
DF_H3K36me3 Man page
DF_H3K36me3_control Man page
DF_H3K4me3 Man page
DF_H3K4me3_ctl Man page
DF_H3K4me3_nopeaks_ratios Man page
.do.normalization Man page
draw.heatmap Man page
draw.heatmap,list-method Man page
draw.heatmap,matrix-method Man page
draw.profile Man page
draw.profile,list-method Man page
draw.profile,matrix-method Man page
export.wig Man page
export.wig,numeric-method Man page
FoxA1_chr19 Man page
genome.covplot.cumdepth Man page
genome.covplot.cumdepth,CoverageBamFile-method Man page
genome.covplot.cumdepth,list-method Man page
genome.covplot.depth Man page
genome.covplot.depth,CoverageBamFile-method Man page
genome.covplot.depth,list-method Man page
.gff.to.GRanges Man page
imageScale Man page
path,CoverageBamFile-method Man page
reads_mapped,CoverageBamFile-method Man page
run_type,CoverageBamFile-method Man page
show,CoverageBamFile-method Man page
show,CoverageBigWigFile-method Man page
write.profile Man page
write.profile,matrix-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.