Files in yue-wang-biomath/RgnTX
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/.Rhistory
R/GRanges2GRangesList.R
R/GRangesList2GRanges.R
R/adjustMultipleTesting.R
R/calculateShift.R
R/distanceTx.R
R/extractRegions.R
R/getStopCodon.R
R/getTransInfo.R
R/globals.R
R/overlapCountsTx.R
R/overlapCountsTxIA.R
R/overlapWidthTx.R
R/permTestTx.R
R/permTestTxIA.R
R/permTestTxIA_customPick.R
R/permTestTx_customAll.R
R/permTestTx_customPick.R
R/plotPermResults.R
R/plotShiftedZScoreTx.R
R/randomizeFeaturesTx.R
R/randomizeFeaturesTxIA.R
R/randomizeTransByOrder.R
R/randomizeTx.R
R/shiftExonTx.R
R/shiftTx.R
R/shiftedZScoreTx.R
R/utility.R
R/vector2GRangesList.R
README.md
inst/extdata/Review/Figure S2 & S3.R
inst/extdata/Review/m7G_methyl_2.rda
inst/extdata/Review/pvals_chi_square.rds
inst/extdata/Review/pvals_default.rds
inst/extdata/Review/pvals_fisher_exact.rds
inst/extdata/Review/pvals_t_test.rds
inst/extdata/Review/simulation_test.R
inst/extdata/m6A_sites_data.rds
inst/extdata/multi_pvals.rds
inst/extdata/permTestTx_results.rds
inst/extdata/permTestTx_results2.rds
inst/extdata/permTestTx_results3.rds
inst/extdata/randomRegionSet1.rds
inst/extdata/randomRegionSet2.rds
inst/extdata/shiftedZScoreTx_results.rds
inst/extdata/transIDs_data.rds
man/GRanges2GRangesList.Rd
man/GRangesList2GRanges.Rd
man/adjustMultipleTesting.Rd
man/calculateShift.Rd
man/distanceTx.Rd
man/extractRegions.Rd
man/getFormatCorrect.Rd
man/getPermSpaceByFeatures.Rd
man/getPermSpaceByTxID.Rd
man/getPermSpaceByType.Rd
man/getPvalZscore.Rd
man/getStopCodon.Rd
man/getTransInfo.Rd
man/overlapCountsTx.Rd
man/overlapCountsTxIA.Rd
man/overlapWidthTx.Rd
man/permTestTx.Rd
man/permTestTxIA.Rd
man/permTestTxIA_customPick.Rd
man/permTestTx_customAll.Rd
man/permTestTx_customPick.Rd
man/plotPermResults.Rd
man/plotShiftedZScoreTx.Rd
man/randomizeFeaturesTx.Rd
man/randomizeFeaturesTxIA.Rd
man/randomizeTransByOrder.Rd
man/randomizeTx.Rd
man/shiftExonTx.Rd
man/shiftTx.Rd
man/shiftedZScoreTx.Rd
man/vector2GRangesList.Rd
tests/testthat.R
tests/testthat/test_evaluation_functions.R
tests/testthat/test_features_process.R
tests/testthat/test_permutation_test_functions.R
tests/testthat/test_randomization_functions.R
vignettes/RgnTX.Rmd
vignettes/figures/section2.1.png
vignettes/figures/section2.2.png
vignettes/figures/section2.3.png
vignettes/figures/section2.4.png
vignettes/figures/section4.1.png
vignettes/figures/section4.2.png
vignettes/figures/section5.2.png
vignettes/figures/section5.5.png
vignettes/figures/section5.6.jpg
vignettes/figures/section7.png
vignettes/figures/section9.1.jpg
vignettes/figures/section9.jpg
