Files in MPIIComputationalEpigenetics/WSHPackage
R package for the calculation of the following Within-Sample Heterogeneity Scores in Bisulfite Sequencing Data: FDRP, qFDRP, PDR, Epipolymorphism, Methylation Entropy and MHL
.Rbuildignore
.gitignore
.travis.yml
BinaryFiles
DESCRIPTION
LICENSE
NAMESPACE
R/calculate_scores.R
R/connect_RnBeads.R
R/main.R
R/run_tools.R
R/utilities.R
README.md
inst/NEWS
inst/bin/methclone
inst/extData/example_GRanges.RData
inst/extData/small_example.bam
inst/extData/small_example.bam.bai
inst/extData/small_rnbSet.zip
inst/scripts/hapinfo2mhl.pl
inst/scripts/mergedBam2hapInfo_RRBS_v1.0.pl
inst/scripts/mergedBam2hapInfo_WGBS_v1.0.pl
inst/unitTests/test_general.R
man/ISH.pdf
man/VALID.SCORES.Rd
man/calculate.entropy.Rd
man/calculate.epipolymorphism.Rd
man/calculate.fdrp.Rd
man/calculate.fdrp.by.chromosome.Rd
man/calculate.fdrp.score.Rd
man/calculate.fdrp.site.Rd
man/calculate.mhl.Rd
man/calculate.pdr.Rd
man/calculate.pdr.by.chromosome.Rd
man/calculate.pdr.site.Rd
man/calculate.qfdrp.Rd
man/compute.score.GRanges.Rd
man/compute.score.Rd
man/compute.score.rnb.Rd
man/create.genomebrowser.track.Rd
man/get.option.Rd
man/rnb.calculate.fdrp.Rd
man/rnb.calculate.mhl.Rd
man/rnb.calculate.pdr.Rd
man/rnb.calculate.qfdrp.Rd
man/run.haplotype.calculation.Rd
man/run.methclone.Rd
man/run.mhl.calculation.Rd
man/set.option.Rd
man/wsh.run.example.Rd
tests/runTests.R
vignettes/WSH.Rnw
vignettes/WSH.md
