CpGindex                Measure methylation status for PRCs or PMDs
ENSR_subset.hg19        ENSR_subset data from hg19 genome
ENSR_subset.hg38        ENSR_subset data from hg38 genome
GRCh37.chromArm         GRCh37.chromArm
GRCh38.chromArm         GRCh38.chromArm
H9state23unmeth.hg19    H9state23unmeth.hg19
H9state23unmeth.hg38    H9state23unmeth.hg38
HMM_CpG_islands.hg19    HMM_CpG_islands.hg19
HMM_CpG_islands.hg38    HMM_CpG_islands.hg38
RRBSeq                  (e)RRBS settings for dmrseq
WGBSage                 Guess ages using Horvath-style 'clock' models
WGBSeq                  Wrapper for WGBS settings for dmrseq
atRegions               Summarize a bsseq dataset over defined regions
binCoverage             Bin CpG or CpH coverage to simplify and improve
                        CNA "sketching"
biscuitMetadata         Biscuit metadata from VCF header
biscuiteer-methods      bsseq class methods (VCF-centric) added by
                        biscuiteer
biscuiteer-package      Convenience Functions for Biscuit
byChromArm              A simple parallization step
byExtremality           Choose loci or features by extremality
checkBiscuitBED         Inspect Biscuit VCF and BED files
clocks                  clocks
condenseSampleNames     Simplify sample names for a bsseq object
extremality             Compute fraction of a Bernoulli variance
fexpit                  Helper function: expanded expit
filterLoci              Filter loci with zero coverage
fixAge                  Turn 'epigenetic clock' into actual age
fixNAs                  Replace NAs with another value
flogit                  Helper function: squeezed logit
getClock                Retrieve 'epigenetic clock' models
getLogitFracMeth        Helper function for compartment inference
grToSeg                 Dump GRanges to segmented data data.frame
hg19.chromArm           hg19.chromArm
hg38.chromArm           hg38.chromArm
makeBSseq               Make an in-memory bsseq object from a biscuit
                        BED
readBiscuit             Read biscuit output into bsseq object
readEpibed              Read in and decode the RLE representation of
                        the epibed format out of biscuit epiread
segToGr                 Import a segmentation file into GRanges object
seqinfo.hg19            seqinfo.hg19
seqinfo.hg38            seqinfo.hg38
seqinfo.mm10            seqinfo.mm10
simplifySampleNames     Simplify bsseq sample names
summarizeBsSeqOver      Summarize methylation over provided regions
tabixRetrieve           Read from tabix-indexed bed file to list
                        objects
unionize                Combine bsseq objects together without losing
                        information
