Files in bsseq

Analyze, manage and store bisulfite sequencing data

README.md R/DelayedArray_utils.R R/BSseq_utils.R R/permutations.R R/hdf5_utils.R R/gof_stats.R R/utils.R R/BSseqStat_class.R R/BSmooth.R R/BSseqTstat_class.R R/read.bsmooth.R R/dmrFinder.R R/hasGRanges.R R/read.bismark.R R/plotting.R R/FWGRanges-class.R R/collapseBSseq.R R/combine.R R/findLoci.R R/getStats.R R/BSmooth.fstat.R R/fisher.R R/BSmooth.tstat.R R/FWIRanges-class.R R/BSseq-class.R vignettes/bsseq.Rmd vignettes/bsseq_analysis.Rmd man/FWGRanges-class.Rd man/BS.chr22.Rd man/goodnessOfFit.Rd man/fisherTests.Rd man/read.bismark.Rd man/BSseq-class.Rd man/getMeth.Rd man/BSmooth.fstat.Rd man/findLoci.Rd man/BSseqStat-class.Rd man/dmrFinder.Rd man/BSmooth.Rd man/smoothSds.Rd man/BSseq.Rd man/BSmooth.tstat.Rd man/plotRegion.Rd man/read.umtab.Rd man/getStats.Rd man/hasGRanges-class.Rd man/internals.Rd man/read.bsmooth.Rd man/data.frame2GRanges.Rd man/computeStat.Rd man/getCoverage.Rd man/BSseqTstat-class.Rd tests/testthat.R tests/testthat/test_BSseq-class.R tests/testthat/test_read.bismark.R tests/testthat/test_GitHub_issues.R tests/testthat/test_perm.R tests/testthat/test_BSmooth.R tests/testthat/test_combine.R tests/testthat/helper_make_test_data.R tests/testthat/test_utils.R tests/testthat/test_base.R tests/testthat/test_check_M_and_Cov.R tests/testthat/test_HDF5_utils.R inst/doc/bsseq.Rmd inst/doc/bsseq_analysis.R inst/doc/bsseq.R inst/doc/bsseq_analysis.Rmd inst/scripts/get_BS.chr22.R