recoup: An R package for the creation of complex genomic profile plots
Version 1.4.0

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>
Bioconductor views ChIPSeq Coverage GeneExpression Preprocessing QualityControl RNASeq Sequencing Software
Date of publicationNone
MaintainerPanagiotis Moulos <moulos@fleming.gr>
LicenseGPL (>= 3)
Version1.4.0
URL https://github.com/pmoulos/recoup
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("recoup")

Getting started

Usage of the recoup package

Popular man pages

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...
getBiotypes: List default Ensembl biotypes
recoupProfile: Plot (faceted) average genomic coverage profiles
recoup_test_data: Reference and genomic sample regions for recoup testing
sliceObj: Subset recoup output list objects
See all...

All man pages Function index File listing

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
mergeRuns: Merge recoup outputs of same type
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

Functions

applySelectors Source code
areColors Source code
baseCoverageMatrix Source code
binCoverageMatrix Source code
buildAnnotationStore Man page Source code
calcCoverage Man page Source code
calcDesignPlotProfiles Source code
calcLinearFactors Source code
calcPlotProfiles Source code
checkFileArgs Source code
checkInput Source code
checkMainArgs Source code
checkNumArgs Source code
checkTextArgs Source code
cleanRanges Source code
cmclapply Source code
cmcmapply Source code
coverageFromBam Source code
coverageFromBigWig Source code
coverageFromBigWigOld Source code
coverageFromRanges Source code
coverageFromRangesOld Source code
coverageRef Man page Source code
coverageRnaRef Man page Source code
decideChanges Source code
getAltHost Source code
getAnnotation Man page Source code
getArg Source code
getBiotypes Man page Source code Source code
getBsOrganism Source code
getDataset Source code
getDefaultListArgs Source code
getEnsemblAnnotation Source code
getExonAttributes Source code
getFlankingRanges Source code
getGcContent Source code
getGeneAttributes Source code
getHost Source code
getMainRanges Source code
getMainRnaRangesOnTheFly Source code
getRegionalRanges Source code
getUcscAnnotation Source code
getUcscCredentials Source code
getUcscDbl Source code
getUcscOrganism Source code Source code
getUcscQuery Source code
getUcscTabledef Source code
getUcscTblTpl Source code
getValidChrs Source code
getValidChrsWithMit Source code
getr Man page Source code
graphicsClose Source code
graphicsOpen Source code
kmeansDesign Man page Source code
loadBsGenome Source code
makeHorizontalAnnotation Source code
mergeRuns Man page Source code
orderDesignSignals Source code
orderProfiles Source code
orderProfilesByDesign Source code
orderSignals Source code
prepareBam Source code
preprocessRanges Man page Source code
profileMatrix Man page Source code
readBam Source code
readBed Source code
readConfig Source code
readRanges Source code
recoup Man page Source code
recoupCorrelation Man page Source code
recoupHeatmap Man page Source code
recoupPlot Man page Source code
recoupProfile Man page Source code
recoup_test_data Man page
reduceExons Source code
removeData Man page Source code
resizeRanges Source code
setArg Source code
setr Man page Source code
sliceObj Man page Source code
splitBySeqname Source code
splitVector Source code
ssCI Source code
test.design Man page
test.exons Man page
test.genome Man page
test.input Man page
toOutput Source code
validateListArgs Source code

Files

DESCRIPTION
NAMESPACE
R
R/annotation.R
R/argcheck.R
R/coverage.R
R/plot.R
R/profile.R
R/ranges.R
R/recoup.R
R/util.R
build
build/vignette.rds
data
data/recoup_test_data.rda
inst
inst/NEWS
inst/doc
inst/doc/recoup_intro.R
inst/doc/recoup_intro.Rmd
inst/doc/recoup_intro.html
inst/extdata
inst/extdata/Set8KO_H4K20me1_50kr.bam
inst/extdata/WT_H4K20me1_50kr.bam
inst/unitTests
inst/unitTests/test_recoup.R
man
man/buildAnnotationStore.Rd
man/calcCoverage.Rd
man/coverageRef.Rd
man/coverageRnaRef.Rd
man/getAnnotation.Rd
man/getBiotypes.Rd
man/kmeansDesign.Rd
man/mergeRuns.Rd
man/preprocessRanges.Rd
man/profileMatrix.Rd
man/recoup.Rd
man/recoupCorrelation.Rd
man/recoupHeatmap.Rd
man/recoupPlot.Rd
man/recoupProfile.Rd
man/recoup_test_data.Rd
man/removeData.Rd
man/simpleGetSet.Rd
man/sliceObj.Rd
tests
tests/runTests.R
vignettes
vignettes/recoup_intro.Rmd
recoup documentation built on May 20, 2017, 9:33 p.m.

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