recoup: An R package for the creation of complex genomic profile plots

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

Author
Panagiotis Moulos <moulos@fleming.gr>
Date of publication
None
Maintainer
Panagiotis Moulos <moulos@fleming.gr>
License
GPL (>= 3)
Version
1.2.0
URLs

View on Bioconductor

Man pages

buildAnnotationStore
Build a local annotation database for recoup
calcCoverage
Calculate coverages over a genomic region
coverageRef
Calculate coverage in a set of reference genomic regions...
coverageRnaRef
Calculate coverage in a set of reference genomic regions...
getAnnotation
Annotation downloader
getBiotypes
List default Ensembl biotypes
kmeansDesign
Apply k-means clustering to profile data
preprocessRanges
Read and preprocess BAM/BED files to GRanges
profileMatrix
Calculate final profile matrices for plotting
recoup
Create genomic signal profiles in predefined or custom areas...
recoupCorrelation
Plot (faceted) average genomic coverage correlations
recoupHeatmap
Plot genomic coverage heatmaps
recoupPlot
Plot list objects returned by recoup
recoupProfile
Plot (faceted) average genomic coverage profiles
recoup_test_data
Reference and genomic sample regions for recoup testing
removeData
Remove data from recoup list object
simpleGetSet
Get and set some reusable objects from a recoup object
sliceObj
Subset recoup output list objects

Files in this package

recoup/DESCRIPTION
recoup/NAMESPACE
recoup/R
recoup/R/annotation.R
recoup/R/argcheck.R
recoup/R/coverage.R
recoup/R/plot.R
recoup/R/profile.R
recoup/R/ranges.R
recoup/R/recoup.R
recoup/R/util.R
recoup/build
recoup/build/vignette.rds
recoup/data
recoup/data/recoup_test_data.rda
recoup/inst
recoup/inst/NEWS
recoup/inst/doc
recoup/inst/doc/recoup_intro.R
recoup/inst/doc/recoup_intro.Rmd
recoup/inst/doc/recoup_intro.html
recoup/inst/extdata
recoup/inst/extdata/Set8KO_H4K20me1_50kr.bam
recoup/inst/extdata/WT_H4K20me1_50kr.bam
recoup/inst/unitTests
recoup/inst/unitTests/test_recoup.R
recoup/man
recoup/man/buildAnnotationStore.Rd
recoup/man/calcCoverage.Rd
recoup/man/coverageRef.Rd
recoup/man/coverageRnaRef.Rd
recoup/man/getAnnotation.Rd
recoup/man/getBiotypes.Rd
recoup/man/kmeansDesign.Rd
recoup/man/preprocessRanges.Rd
recoup/man/profileMatrix.Rd
recoup/man/recoup.Rd
recoup/man/recoupCorrelation.Rd
recoup/man/recoupHeatmap.Rd
recoup/man/recoupPlot.Rd
recoup/man/recoupProfile.Rd
recoup/man/recoup_test_data.Rd
recoup/man/removeData.Rd
recoup/man/simpleGetSet.Rd
recoup/man/sliceObj.Rd
recoup/tests
recoup/tests/runTests.R
recoup/vignettes
recoup/vignettes/recoup_intro.Rmd