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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CoverageView")
AuthorErnesto Lowy
Bioconductor views ChIPSeq RNASeq Sequencing Software Technology Visualization
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

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