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

Functions

buildAnnotationStore Man page
calcCoverage Man page
coverageRef Man page
coverageRnaRef Man page
getAnnotation Man page
getBiotypes Man page
getr Man page
kmeansDesign Man page
preprocessRanges Man page
profileMatrix Man page
recoup Man page
recoupCorrelation Man page
recoupHeatmap Man page
recoupPlot Man page
recoupProfile Man page
recoup_test_data Man page
removeData Man page
setr Man page
sliceObj Man page
test.design Man page
test.exons Man page
test.genome Man page
test.input Man page

Files

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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