Files in bernatgel/regioneR
Association analysis of genomic regions based on permutation tests
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/characterToBSGenome.R
R/circularRandomizeRegions.R
R/commonRegions.R
R/createFunctionsList.R
R/createRandomRegions.R
R/emptyCacheRegioneR.R
R/extendRegions.R
R/filterChromosomes.R
R/getChromosomesByOrganism.R
R/getGenome.R
R/getGenomeAndMask.R
R/getMask.R
R/joinRegions.R
R/listChrTypes.R
R/localZScore.R
R/maskFromBSGenome.R
R/meanDistance.R
R/meanInRegions.R
R/mergeRegions.R
R/numOverlaps.R
R/overlapGraphicalSummary.R
R/overlapPermTest.R
R/overlapRegions.R
R/permTest.R
R/plot.localZScoreResults.R
R/plot.localZScoreResultsList.R
R/plot.permTestResults.R
R/plot.permTestResultsList.R
R/plotRegions.R
R/print.permTestResults.R
R/randomizeRegions.R
R/recomputePermTest.R
R/resampleGenome.R
R/resampleRegions.R
R/splitRegions.R
R/subtractRegions.R
R/summary.permTestResults.R
R/summary.permTestResultsList.R
R/toDataframe.R
R/toGRanges.R
R/uniqueRegions.R
R/utils.R
inst/CITATION
inst/extdata/all.genes.txt
inst/extdata/my.altered.regions.txt
inst/extdata/my.regular.genes.txt
inst/extdata/my.special.genes.txt
man/characterToBSGenome.Rd
man/circularRandomizeRegions.Rd
man/commonRegions.Rd
man/createFunctionsList.Rd
man/createRandomRegions.Rd
man/emptyCacheRegioneR.Rd
man/extendRegions.Rd
man/filterChromosomes.Rd
man/getChromosomesByOrganism.Rd
man/getGenome.Rd
man/getGenomeAndMask.Rd
man/getMask.Rd
man/joinRegions.Rd
man/listChrTypes.Rd
man/localZScore.Rd
man/maskFromBSGenome.Rd
man/meanDistance.Rd
man/meanInRegions.Rd
man/mergeRegions.Rd
man/numOverlaps.Rd
man/overlapGraphicalSummary.Rd
man/overlapPermTest.Rd
man/overlapRegions.Rd
man/permTest.Rd
man/plot.localZScoreResults.Rd
man/plot.localZScoreResultsList.Rd
man/plot.permTestResults.Rd
man/plot.permTestResultsList.Rd
man/plotRegions.Rd
man/print.permTestResults.Rd
man/randomizeRegions.Rd
man/recomputePermTest.Rd
man/resampleGenome.Rd
man/resampleRegions.Rd
man/splitRegions.Rd
man/subtractRegions.Rd
man/summary.permTestResults.Rd
man/summary.permTestResultsList.Rd
man/toDataframe.Rd
man/toGRanges.Rd
man/uniqueRegions.Rd
tests/testthat.R
tests/testthat/test_data_files/4columns.bed
tests/testthat/test_data_files/4columns.txt
tests/testthat/test_data_files/alt_sep1.txt
tests/testthat/test_data_files/alt_sep2.txt
tests/testthat/test_data_files/alt_sep2_with_other_seps.txt
tests/testthat/test_data_files/bed_with_header.bed
tests/testthat/test_data_files/comments_and_header.txt
tests/testthat/test_data_files/empty_file.txt
tests/testthat/test_data_files/noheader.txt
tests/testthat/test_data_files/only_comments.txt
tests/testthat/test_data_files/only_comments_and_header.txt
tests/testthat/test_data_files/regs.bed
tests/testthat/test_data_files/regs.txt
tests/testthat/test_data_files/two_valid_seps.txt
tests/testthat/test_evaluationFunctions.R
tests/testthat/test_genomesAndMasks.R
tests/testthat/test_numOverlaps.R
tests/testthat/test_permTest.R
tests/testthat/test_randomizationFunctions.R
tests/testthat/test_toGRanges.R
vignettes/figures/Example1_fig1.pdf
vignettes/figures/Example1_fig1.png
vignettes/figures/Example2_fig1.pdf
vignettes/figures/Example2_fig1.png
vignettes/figures/Example2_fig2.pdf
vignettes/figures/Example2_fig2.png
vignettes/figures/Example2_fig3.pdf
vignettes/figures/Example2_fig3.png
vignettes/figures/Example2_fig4.pdf
vignettes/figures/Example2_fig4.png
vignettes/figures/mask_test_regioneR_small.pdf
vignettes/figures/mask_test_regioneR_small.png
vignettes/figures/regular_genes_5000perm.pdf
vignettes/figures/regular_genes_5000perm.png
vignettes/figures/special_genes_5000perm.pdf
vignettes/figures/special_genes_5000perm.png
vignettes/figures/speed_test_regioneR_small.pdf
vignettes/figures/speed_test_regioneR_small.png
vignettes/regioneR.Rmd
