CoverageView: Coverage visualization package for R
Version 1.12.0

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

Browse man pages Browse package API and functions Browse package files

AuthorErnesto Lowy
Bioconductor views ChIPSeq RNASeq Sequencing Software Technology Visualization
Date of publicationNone
MaintainerErnesto Lowy <ernestolowy@gmail.com>
LicenseArtistic-2.0
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CoverageView")

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

Functions

.bed.to.GRanges Man page
.cov.bin Man page
.do.normalization Man page
.gff.to.GRanges Man page
CoverageBamFile Man page Source code
CoverageBamFile-class Man page
CoverageBigWigFile Man page Source code
CoverageBigWigFile-class Man page
CoverageView Man page
CoverageView-internal Man page
CoverageView-package 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
FoxA1_chr19 Man page
bed.to.GRanges Source code
checkErrors Source code
cov.bin Man page Source code
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,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,CoverageBamFile,characte Man page
cov.bin,missing,missing,missing,missing,character-method Man page
cov.bin-methods 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
defaultCores Source code
do.normalization Source code
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 Source code
export.wig,numeric-method 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 Source code
imageScale Man page Source code
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
CoverageView documentation built on May 20, 2017, 9:18 p.m.