Package: recoup 1.35.0

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]>

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recoup.pdf |recoup.html✨
recoup/json (API)
NEWS

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

Peer review:

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-1.35.0(bioc 3.21)recoup-1.34.0(bioc 3.20)

immunooncologysoftwaregeneexpressionpreprocessingqualitycontrolrnaseqchipseqsequencingcoverageatacseqchiponchipalignmentdataimport

5.02 score 1 stars 2 scripts 205 downloads 1 mentions 25 exports 116 dependencies

Last updated 2 months agofrom:8112b7eaff. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 17 2024
R-4.5-winNOTEDec 17 2024
R-4.5-linuxNOTEDec 17 2024
R-4.4-winNOTEDec 17 2024
R-4.4-macNOTEDec 17 2024
R-4.3-winNOTEDec 17 2024
R-4.3-macNOTEDec 17 2024

Exports:buildAnnotationDatabasebuildAnnotationStorebuildCustomAnnotationcalcCoveragecoverageRefcoverageRnaRefgetAnnotationgetBiotypesgetInstalledAnnotationsgetrimportCustomAnnotationkmeansDesignloadAnnotationmergeRunspreprocessRangesprofileMatrixrecouprecoupCorrelationrecoupHeatmaprecoupPlotrecoupProfileremoveDatarpMatrixsetrsliceObj

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArraydigestdoParalleldplyrfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzlibbioc

Usage of the recoup package

Panagiotis Moulos

Rendered fromrecoup_intro.Rmdusingknitr::rmarkdownon Dec 17 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Build a local annotation database for recoupbuildAnnotationDatabase
Build a local annotation database for recoupbuildAnnotationStore
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
Defunct functions in package 'recoup'recoup-defunct
Deprecated functions in package 'recoup'recoup-deprecated
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