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.gitignore
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.Rproj.user
.Rhistory
.RData
.Ruserdata
*.history
data-raw/GSE63179/GSE63179_RAW.tar
data-raw/GSE63179/GSE63179_matrixSignalIntensities.txt.gz
data-raw/GSE63179/idat/GSM1543269_9373551079_R01C01_Grn.idat
data-raw/GSE63179/idat/GSM1543269_9373551079_R01C01_Red.idat
data-raw/GSE63179/idat/GSM1543270_9373551079_R01C02_Grn.idat
*.idat
data-raw/rgSet.rds
data-raw/pD.rds
data-raw/GSE63179/filelist.txt
data-raw/GSE63179/idat/GPL16304_Gene_features_Metadata.txt.gz
data-raw/GSE63179/idat/GPL16304_Gene_features_PlatformTable.txt.gz
data-raw/example2/GSE73895/GSE73895_RAW.tar
data-raw/example2/GSE73895/idat/GPL13534_450K_Manifest_header_Descriptions.xlsx.gz
data-raw/example2/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.1.bpm.txt.gz
data-raw/example2/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.1.csv.gz
data-raw/example2/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.2.bpm.gz
data-raw/example2/GSE73895/filelist.txt
data-raw/example2/MethOxy.rds
data-raw/example1/GSE63179/filelist.txt
data-raw/example1/GSE63179/GSE63179_matrixSignalIntensities.txt.gz
data-raw/example1/GSE63179/GSE63179_RAW.tar
data-raw/example1/GSE63179/idat/GPL16304_Gene_features_Metadata.txt.gz
data-raw/example1/GSE63179/idat/GPL16304_Gene_features_PlatformTable.txt.gz
data-raw/example1/rgSet.rds
vignettes/vignette.toc
vignettes/vignette.pdf
vignettes/vignette.out
vignettes/vignette.aux
vignettes/vignette.blg
vignettes/vignette.bbl
vignettes/vignette.log
vignettes/MethylatedBS.rds
vignettes/MethylatedBS2.rds
vignettes/MethylatedOxBS2.rds
vignettes/results_emPD2.rds
vignettes/results_emPD1.rds
vignettes/UnMethylatedOxBS2.rds
vignettes/vignette-fig10.pdf
vignettes/vignette-fig11.pdf
vignettes/UnMethylatedBS.rds
vignettes/UnMethylatedBS2.rds
vignettes/pD1.rds
vignettes/pD.rds
vignettes/MethylatedOxBS.rds
vignettes/UnMethylatedOxBS.rds
data-raw/vignette_old/MethylatedBS.rds
data-raw/vignette_old/MethylatedBS2.rds
data-raw/vignette_old/MethylatedOxBS2.rds
data-raw/vignette_old/pD1.rds
data-raw/vignette_old/results_emPD1.rds
data-raw/vignette_old/results_emPD2.rds
data-raw/vignette_old/pD.rds
data-raw/vignette_old/UnMethylatedOxBS2.rds
data-raw/vignette_old/UnMethylatedOxBS.rds
data-raw/vignette_old/UnMethylatedBS2.rds
data-raw/vignette_old/UnMethylatedBS.rds
data-raw/vignette_old/MethylatedOxBS.rds
vignettes/GSE63179/filelist.txt
vignettes/GSE63179/GSE63179_matrixSignalIntensities.txt.gz
vignettes/GSE63179/GSE63179_RAW.tar
vignettes/GSE63179/idat/GPL16304_Gene_features_Metadata.txt.gz
vignettes/GSE63179/idat/GPL16304_Gene_features_PlatformTable.txt.gz
vignettes/GSE73895/filelist.txt
vignettes/GSE73895/GSE73895_RAW.tar
vignettes/GSE73895/idat/GPL13534_450K_Manifest_header_Descriptions.xlsx.gz
vignettes/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.1.bpm.txt.gz
vignettes/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.1.csv.gz
vignettes/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.2.bpm.gz
data-raw/vignette_realdata/GSE63179/filelist.txt
data-raw/vignette_realdata/vignette.bbl
data-raw/vignette_realdata/vignette-fig11.pdf
data-raw/vignette_realdata/pD.rds
data-raw/vignette_realdata/pD1.rds
data-raw/vignette_realdata/refs.bib
data-raw/vignette_realdata/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.2.bpm.gz
data-raw/vignette_realdata/GSE73895/idat/GPL13534_450K_Manifest_header_Descriptions.xlsx.gz
data-raw/vignette_realdata/GSE73895/GSE73895_RAW.tar
data-raw/vignette_realdata/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.1.csv.gz
data-raw/vignette_realdata/GSE73895/filelist.txt
data-raw/vignette_realdata/vignette-fig10.pdf
data-raw/vignette_realdata/GSE63179/idat/GPL16304_Gene_features_PlatformTable.txt.gz
data-raw/vignette_realdata/GSE63179/idat/GPL16304_Gene_features_Metadata.txt.gz
data-raw/vignette_realdata/GSE63179/GSE63179_matrixSignalIntensities.txt.gz
data-raw/vignette_realdata/GSE63179/GSE63179_RAW.tar
data-raw/vignette_realdata/GSE73895/idat/GPL13534_HumanMethylation450_15017482_v.1.1.bpm.txt.gz
data-raw/vignette_realdata/vignette.log
data-raw/vignette_realdata/vignette.toc
data-raw/vignette_realdata/vignette.pdf
data-raw/vignette_realdata/vignette.Rnw
inst/doc
data-raw/simulatedCounts/0.1-0.1.rda
data-raw/simulatedCounts/0.1-0.1.rda
data-raw/simulatedCounts/0.3-0.1.rda
data-raw/simulatedCounts/0.3-0.1.rda
data-raw/simulatedCounts/0.1-0.1.rda
data-raw/Input.rds
data-raw/README.html
vignettes/GSE71398/filelist.txt
vignettes/GSE71398/GSE71398_RAW.tar
*.gz
vignettes/data_processed1.rds
data-raw/GSE71398/filelist.txt
data-raw/GSE71398/GSE71398_RAW.tar
*.txt
data-raw/example4/BS-seq.Rds
data-raw/example4/GSE70090/GSE70090_RAW.tar
data-raw/example4/oxBS-seq.Rds
data-raw/example4/MethOxy.rds
data-raw/example4/mbm.rds
data-raw/example4/results_em.rds
data-raw/example4/results_exact.rds
data-raw/example4/results_naive.rds
data-raw/example4/results_naive1.rds
data-raw/example4/results_em1.rds
data-raw/example4/results_exact1.rds
.DS_Store