Files in hansenlab/bsseq
Analyze, manage and store whole-genome methylation data
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/BSmooth.R
R/BSmooth.fstat.R
R/BSmooth.tstat.R
R/BSseq-class.R
R/BSseqStat_class.R
R/BSseqTstat_class.R
R/BSseq_utils.R
R/DelayedArray_utils.R
R/FWGRanges-class.R
R/FWIRanges-class.R
R/collapseBSseq.R
R/combine.R
R/dmrFinder.R
R/findLoci.R
R/fisher.R
R/getStats.R
R/gof_stats.R
R/hasGRanges.R
R/hdf5_utils.R
R/permutations.R
R/plotting.R
R/read.bismark.R
R/read.modbam2bed.R
R/read.modkit.R
R/utils.R
README.md
bsseq.Rproj
data/BS.chr22.rda
inst/CITATION
inst/NEWS.Rd
inst/extdata/modbam2bed/ctr1.chr10.chr11.bed.gz
inst/extdata/modbam2bed/ctr2.chr10.chr11.bed.gz
inst/extdata/modbam2bed/ctr3.chr10.chr11.bed.gz
inst/extdata/modbam2bed/tret1.chr10.chr11.bed.gz
inst/extdata/modbam2bed/tret2.chr10.chr11.bed.gz
inst/extdata/modbam2bed/tret3.chr10.chr11.bed.gz
inst/extdata/modkit/Hypo1.first50Bed.txt
inst/extdata/modkit/chr21.chr22.HG002.top1000.bed.gz
inst/extdata/test_data.cytosineReport.gz
inst/extdata/test_data.fastq_bismark.bismark.cov.gz
inst/scripts/get_BS.chr22.R
man/BS.chr22.Rd
man/BSmooth.Rd
man/BSmooth.fstat.Rd
man/BSmooth.tstat.Rd
man/BSseq-class.Rd
man/BSseq.Rd
man/BSseqStat-class.Rd
man/BSseqTstat-class.Rd
man/FWGRanges-class.Rd
man/computeStat.Rd
man/data.frame2GRanges.Rd
man/dmrFinder.Rd
man/findLoci.Rd
man/fisherTests.Rd
man/getCoverage.Rd
man/getMeth.Rd
man/getStats.Rd
man/goodnessOfFit.Rd
man/hasGRanges-class.Rd
man/internals.Rd
man/plotRegion.Rd
man/read.bismark.Rd
man/read.modbam2bed.Rd
man/read.modkit.Rd
man/smoothSds.Rd
src/.gitignore
src/BSseq.h
src/check_M_and_Cov.cpp
src/init.cpp
src/utils.cpp
src/utils.h
tests/testthat.R
tests/testthat/helper_make_test_data.R
tests/testthat/test_BSmooth.R
tests/testthat/test_BSseq-class.R
tests/testthat/test_GitHub_issues.R
tests/testthat/test_HDF5_utils.R
tests/testthat/test_base.R
tests/testthat/test_check_M_and_Cov.R
tests/testthat/test_combine.R
tests/testthat/test_perm.R
tests/testthat/test_read.bismark.R
tests/testthat/test_read.modbam2bed.R
tests/testthat/test_read.modkit.R
tests/testthat/test_utils.R
vignettes/bsseq.Rmd
vignettes/bsseq.bib
vignettes/bsseq_analysis.Rmd
vignettes/unsrturl.bst
