Package: recoup 1.41.0

Panagiotis Moulos

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.

Authors:Panagiotis Moulos <[email protected]>

recoup_1.41.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
recoup/json (API)
NEWS

# Install 'recoup' in R:
install.packages('recoup', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pmoulos/recoup/issues

Datasets:
  • test.design - Reference and genomic sample regions for recoup testing
  • test.exons - Reference and genomic sample regions for recoup testing
  • test.genome - Reference and genomic sample regions for recoup testing
  • test.input - Reference and genomic sample regions for recoup testing

On BioConductor:recoup-1.41.0(bioc 3.24)recoup-1.40.0(bioc 3.23)

immunooncologysoftwaregeneexpressionpreprocessingqualitycontrolrnaseqchipseqsequencingcoverageatacseqchiponchipalignmentdataimport

5.24 score 1 stars 7 scripts 426 downloads 1 mentions 24 exports 112 dependencies

Last updated from:ad7ae07e1e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR184
linux-devel-x86_64NOTE529
source / vignettesOK290
linux-release-x86_64NOTE501
macos-release-arm64NOTE252
macos-oldrel-arm64NOTE390
windows-develNOTE419
windows-releaseNOTE443
windows-oldrelNOTE395
wasm-releaseOK151

Exports:buildAnnotationDatabasebuildCustomAnnotationcalcCoveragecoverageRefcoverageRnaRefgetAnnotationgetBiotypesgetInstalledAnnotationsgetrimportCustomAnnotationkmeansDesignloadAnnotationmergeRunspreprocessRangesprofileMatrixrecouprecoupCorrelationrecoupHeatmaprecoupPlotrecoupProfileremoveDatarpMatrixsetrsliceObj

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArraydigestdoParalleldplyrfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryaml

Usage of the recoup package

Panagiotis Moulos

Rendered fromrecoup_intro.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2020-05-04
Started: 2016-03-23

Readme and manuals

Help Manual

Help pageTopics
Build a local annotation database for recoupbuildAnnotationDatabase
Import custom annotation to the recoup annotation database from GTF filebuildCustomAnnotation
Calculate coverages over a genomic regioncalcCoverage
Calculate coverage in a set of reference genomic regions (ChIP-Seq or unspliced mode)coverageRef
Calculate coverage in a set of reference genomic regions (RNA-Seq or spliced mode)coverageRnaRef
Annotation downloadergetAnnotation
List default Ensembl biotypesgetBiotypes
Load a recoup annotation elementgetInstalledAnnotations
Import a recoup custom annotation elementimportCustomAnnotation
Apply k-means clustering to profile datakmeansDesign
Load a recoup annotation elementloadAnnotation
Merge recoup outputs of same typemergeRuns
Read and preprocess BAM/BED files to GRangespreprocessRanges
Calculate final profile matrices for plottingprofileMatrix
Create genomic signal profiles in predefined or custom areas using short sequence readsrecoup
Reference and genomic sample regions for recoup testingrecoup_test_data test.design test.exons test.genome test.input
Plot (faceted) average genomic coverage correlationsrecoupCorrelation
Plot genomic coverage heatmapsrecoupHeatmap
Plot list objects returned by recouprecoupPlot
Plot (faceted) average genomic coverage profilesrecoupProfile
Remove data from recoup list objectremoveData
Reads per million profile matrices for plottingrpMatrix
Get and set some reusable objects from a recoup objectgetr setr
Subset recoup output list objectssliceObj