atRegions               Summarize a bsseq dataset over defined regions
binCoverage             Bin CpG or CpH coverage to simplify and improve
                        CNA "sketching"
biscuiteer-methods      bsseq class methods (VCF-centric) added by
                        biscuiteer
biscuiteer-package      Convenience Functions for Biscuit
biscuitMetadata         Biscuit metadata from VCF header
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
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
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
GRCh37.chromArm         GRCh37.chromArm
GRCh38.chromArm         GRCh38.chromArm
grToSeg                 Dump GRanges to segmented data data.frame
H9state23unmeth.hg19    H9state23unmeth.hg19
H9state23unmeth.hg38    H9state23unmeth.hg38
hg19.chromArm           hg19.chromArm
hg38.chromArm           hg38.chromArm
HMM_CpG_islands.hg19    HMM_CpG_islands.hg19
HMM_CpG_islands.hg38    HMM_CpG_islands.hg38
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
RRBSeq                  (e)RRBS settings for dmrseq
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
WGBSage                 Guess ages using Horvath-style 'clock' models
WGBSeq                  Wrapper for WGBS settings for dmrseq
