Package: regioneR 1.37.0

Bernat Gel

regioneR: Association analysis of genomic regions based on permutation tests

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

Authors:Anna Diez-Villanueva <[email protected]>, Roberto Malinverni <[email protected]> and Bernat Gel <[email protected]>

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regioneR.pdf |regioneR.html✨
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NEWS

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

Peer review:

On BioConductor:regioneR-1.37.0(bioc 3.20)regioneR-1.36.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

34 exports 3.40 score 54 dependencies 20 dependents 30 mentions

Last updated 2 months agofrom:d6368f7a29

Exports:characterToBSGenomecircularRandomizeRegionscommonRegionscreateFunctionsListcreateRandomRegionsemptyCacheRegioneRextendRegionsfilterChromosomesgetChromosomesByOrganismgetGenomegetGenomeAndMaskgetMaskjoinRegionslistChrTypeslocalZScoremaskFromBSGenomemeanDistancemeanInRegionsmergeRegionsnumOverlapsoverlapGraphicalSummaryoverlapPermTestoverlapRegionspermTestplotRegionsrandomizeRegionsrecomputePermTestresampleGenomeresampleRegionssplitRegionssubtractRegionstoDataframetoGRangesuniqueRegions

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecachemcodetoolscpp11crayoncurlDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmemoisemimeopensslR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

regioneR: Association analysis of genomic regions based on permutation tests

Bernat Gel ([email protected]), Anna Diez-Villanueva ([email protected]) and Roberto Malinverni ([email protected])

Rendered fromregioneR.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-07-16
Started: 2018-08-13

Readme and manuals

Help Manual

Help pageTopics
characterToBSGenomecharacterToBSGenome
Circular Randomize RegionscircularRandomizeRegions
Common RegionscommonRegions
Create Functions ListcreateFunctionsList
Create Random RegionscreateRandomRegions
Empty Cache regioneRemptyCacheRegioneR
Extend RegionsextendRegions
filterChromosomesfilterChromosomes
getChromosomesByOrganismgetChromosomesByOrganism
getGenomegetGenome
getGenomeAndMaskgetGenomeAndMask
getMaskgetMask
Join RegionsjoinRegions
filterChromosomes listChrTypeslistChrTypes
Local z-scorelocalZScore
maskFromBSGenomemaskFromBSGenome
Mean DistancemeanDistance
Mean In RegionsmeanInRegions
Merge RegionsmergeRegions
Number Of OverlapsnumOverlaps
Overlap Graphical SummaryoverlapGraphicalSummary
Permutation Test for OverlapoverlapPermTest
Overlap RegionsoverlapRegions
Permutation TestpermTest
Plot localZscore resultsplot.localZScoreResults
Function for plotting the results from a 'permTestResults' object.plot.permTestResults
Function for plotting the results from a 'permTestResultsList' object when more than one evaluation function was used.plot.permTestResultsList
Plot RegionsplotRegions
Randomize RegionsrandomizeRegions
Recompute Permutation TestrecomputePermTest
resampleGenomeresampleGenome
Resample RegionsresampleRegions
Split RegionssplitRegions
Subtract RegionssubtractRegions
toDataframetoDataframe
toGRangestoGRanges
Unique RegionsuniqueRegions