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.

AuthorPanagiotis Moulos <moulos@fleming.gr>
Date of publicationNone
MaintainerPanagiotis Moulos <moulos@fleming.gr>
LicenseGPL (>= 3)
Version1.2.0
https://github.com/pmoulos/recoup

View on Bioconductor

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

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

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