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.

AuthorAnna Diez-Villanueva <adiez@imppc.org>, Roberto Malinverni <rmalinverni@carrerasresearch.org> and Bernat Gel <bgel@imppc.org>
Date of publicationNone
MaintainerBernat Gel <bgel@imppc.org>
LicenseArtistic-2.0
Version1.6.0

View on Bioconductor

Man pages

characterToBSGenome: characterToBSGenome

circularRandomizeRegions: Circular Randomize Regions

commonRegions: Common Regions

createFunctionsList: Create Functions List

createRandomRegions: Create Random Regions

emptyCacheRegioneR: Empty Cache regioneR

extendRegions: Extend Regions

filterChromosomes: filterChromosomes

getChromosomesByOrganism: getChromosomesByOrganism

getGenome: getGenome

getGenomeAndMask: getGenomeAndMask

getMask: getMask

joinRegions: Join Regions

listChrTypes: filterChromosomes listChrTypes

localZScore: Local z-score

maskFromBSGenome: maskFromBSGenome

meanDistance: Mean Distance

meanInRegions: Mean In Regions

mergeRegions: Merge Regions

numOverlaps: Number Of Overlaps

overlapGraphicalSummary: Overlap Graphical Summary

overlapPermTest: Permutation Test for Overlap

overlapRegions: Overlap Regions

permTest: Permutation Test

plot.localZScoreResults: Plot localZscore results

plot.localZScoreResultsList: Plot a list of localZscore results

plot.permTestResults: Function for plotting the results from a 'permTestResults'...

plot.permTestResultsList: Function for plotting the results from a...

plotRegions: Plot Regions

print.permTestResults: Print permTestResults objects

randomizeRegions: Randomize Regions

recomputePermTest: Recompute Permutation Test

resampleRegions: Resample Regions

splitRegions: Split Regions

subtractRegions: Subtract Regions

summary.permTestResults: Summary of permTestResults objects

summary.permTestResultsList: Summary of permTestResultsList objects

toDataframe: toDataframe

toGRanges: toGRanges

uniqueRegions: Unique Regions

Files in this package

regioneR/DESCRIPTION
regioneR/NAMESPACE
regioneR/NEWS
regioneR/R
regioneR/R/characterToBSGenome.R regioneR/R/circularRandomizeRegions.R regioneR/R/commonRegions.R regioneR/R/createFunctionsList.R regioneR/R/createRandomRegions.R regioneR/R/emptyCacheRegioneR.R regioneR/R/extendRegions.R regioneR/R/filterChromosomes.R regioneR/R/getChromosomesByOrganism.R regioneR/R/getGenome.R regioneR/R/getGenomeAndMask.R regioneR/R/getMask.R regioneR/R/joinRegions.R regioneR/R/listChrTypes.R regioneR/R/localZScore.R regioneR/R/maskFromBSGenome.R regioneR/R/meanDistance.R regioneR/R/meanInRegions.R regioneR/R/mergeRegions.R regioneR/R/numOverlaps.R regioneR/R/overlapGraphicalSummary.R regioneR/R/overlapPermTest.R regioneR/R/overlapRegions.R regioneR/R/permTest.R regioneR/R/plot.localZScoreResults.R regioneR/R/plot.localZScoreResultsList.R regioneR/R/plot.permTestResults.R regioneR/R/plot.permTestResultsList.R regioneR/R/plotRegions.R regioneR/R/print.permTestResults.R regioneR/R/randomizeRegions.R regioneR/R/recomputePermTest.R regioneR/R/resampleRegions.R regioneR/R/splitRegions.R regioneR/R/subtractRegions.R regioneR/R/summary.permTestResults.R regioneR/R/summary.permTestResultsList.R regioneR/R/toDataframe.R regioneR/R/toGRanges.R regioneR/R/uniqueRegions.R
regioneR/build
regioneR/build/vignette.rds
regioneR/inst
regioneR/inst/CITATION
regioneR/inst/doc
regioneR/inst/doc/regioneR.R
regioneR/inst/doc/regioneR.Rnw
regioneR/inst/doc/regioneR.pdf
regioneR/inst/extdata
regioneR/inst/extdata/all.genes.bed
regioneR/inst/extdata/my.altered.regions.bed
regioneR/inst/extdata/my.special.genes.bed
regioneR/man
regioneR/man/characterToBSGenome.Rd regioneR/man/circularRandomizeRegions.Rd regioneR/man/commonRegions.Rd regioneR/man/createFunctionsList.Rd regioneR/man/createRandomRegions.Rd regioneR/man/emptyCacheRegioneR.Rd regioneR/man/extendRegions.Rd regioneR/man/filterChromosomes.Rd regioneR/man/getChromosomesByOrganism.Rd regioneR/man/getGenome.Rd regioneR/man/getGenomeAndMask.Rd regioneR/man/getMask.Rd regioneR/man/joinRegions.Rd regioneR/man/listChrTypes.Rd regioneR/man/localZScore.Rd regioneR/man/maskFromBSGenome.Rd regioneR/man/meanDistance.Rd regioneR/man/meanInRegions.Rd regioneR/man/mergeRegions.Rd regioneR/man/numOverlaps.Rd regioneR/man/overlapGraphicalSummary.Rd regioneR/man/overlapPermTest.Rd regioneR/man/overlapRegions.Rd regioneR/man/permTest.Rd regioneR/man/plot.localZScoreResults.Rd regioneR/man/plot.localZScoreResultsList.Rd regioneR/man/plot.permTestResults.Rd regioneR/man/plot.permTestResultsList.Rd regioneR/man/plotRegions.Rd regioneR/man/print.permTestResults.Rd regioneR/man/randomizeRegions.Rd regioneR/man/recomputePermTest.Rd regioneR/man/resampleRegions.Rd regioneR/man/splitRegions.Rd regioneR/man/subtractRegions.Rd regioneR/man/summary.permTestResults.Rd regioneR/man/summary.permTestResultsList.Rd regioneR/man/toDataframe.Rd regioneR/man/toGRanges.Rd regioneR/man/uniqueRegions.Rd
regioneR/tests
regioneR/tests/testthat
regioneR/tests/testthat.R
regioneR/tests/testthat/test_evaluationFunctions.R
regioneR/tests/testthat/test_genomesAndMasks.R
regioneR/tests/testthat/test_numOverlaps.R
regioneR/tests/testthat/test_permTest.R
regioneR/tests/testthat/test_randomizationFunctions.R
regioneR/vignettes
regioneR/vignettes/figures
regioneR/vignettes/figures/Example1_fig1.pdf
regioneR/vignettes/figures/Example2_fig1.pdf
regioneR/vignettes/figures/Example2_fig2.pdf
regioneR/vignettes/figures/Example2_fig3.pdf
regioneR/vignettes/figures/Example2_fig4.pdf
regioneR/vignettes/figures/mask_test_regioneR_small.pdf
regioneR/vignettes/figures/regular_genes_5000perm.pdf
regioneR/vignettes/figures/special_genes_5000perm.pdf
regioneR/vignettes/figures/speed_test_regioneR_small.pdf
regioneR/vignettes/regioneR.Rnw

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