regioneR: Association analysis of genomic regions based on permutation tests

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

Author
Anna Diez-Villanueva <adiez@imppc.org>, Roberto Malinverni <rmalinverni@carrerasresearch.org> and Bernat Gel <bgel@imppc.org>
Date of publication
None
Maintainer
Bernat Gel <bgel@imppc.org>
License
Artistic-2.0
Version
1.6.0

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