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
Version1.6.2

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

Functions

characterToBSGenome Man page
circularRandomizeRegions Man page
commonRegions Man page
createFunctionsList Man page
createRandomRegions Man page
emptyCacheRegioneR Man page
extendRegions Man page
filterChromosomes Man page
getChromosomesByOrganism Man page
getGenome Man page
getGenomeAndMask Man page
getMask Man page
joinRegions Man page
listChrTypes Man page
localZScore Man page
maskFromBSGenome Man page
meanDistance Man page
meanInRegions Man page
mergeRegions Man page
numOverlaps Man page
overlapGraphicalSummary Man page
overlapPermTest Man page
overlapRegions Man page
permTest Man page
plot.localZScoreResults Man page
plot.localZScoreResultsList Man page
plot.permTestResults Man page
plot.permTestResultsList Man page
plotRegions Man page
print.permTestResults Man page
randomizeRegions Man page
recomputePermTest Man page
resampleRegions Man page
splitRegions Man page
subtractRegions Man page
summary.permTestResults Man page
summary.permTestResultsList Man page
toDataframe Man page
toGRanges Man page
uniqueRegions Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.