.calculate_regions_intersections
                        Calculate the number of bases in the
                        intersection of two GRanges objects
.chunk_regions          Split genomic regions into balanced chunks
                        based on the number of methylation sites that
                        they cover
.count_covered_bases    Calculate the number of unique bases covered by
                        all regions in a GRanges object
.find_tmrs_single       Find TSS-Proximal Methylation-Controlled
                        Regulatory Sites (TMRs)
.summarize_chunk_methylation
                        Summarize methylation values for regions in a
                        chunk
.test_tmrs              Find TMRs where smoothed methodical scores
                        exceed thresholds
.tss_correlations       Calculate meth site-transcript correlations for
                        given TSS
.tss_iterator           Create an iterator function for use with
                        bpiterate
TumourMethDatasets      TumourMethDatasets
annotateGRanges         Annotate GRanges
annotatePlot            Create a plot with genomic annotation for a
                        plot of values at methylation sites.
calculateMethSiteTranscriptCors
                        Calculate correlation between expression of
                        transcripts and methylation of sites
                        surrounding their TSS
calculateRegionMethylationTranscriptCors
                        Calculate the correlation values between the
                        methylation of genomic regions and the
                        expression of associated transcripts
calculateSmoothedMethodicalScores
                        Calculate methodical score and smooth it using
                        a exponential weighted moving average
correct_correlation_pvalues
                        Correct p-values for a list of
                        methylation-transcription correlations results
createRandomRegions     Create a GRanges with random regions from a
                        genome
expand_granges          Expand GRanges
extractGRangesMethSiteValues
                        Extract values for methylation sites
                        overlapping genomic regions from a methylation
                        RSE.
extractMethSitesFromGenome
                        Create a GRanges with methylation sites of
                        interest from a BSgenome.
findTMRs                Find TSS-Proximal Methylation-Controlled
                        Regulatory Sites (TMRs)
hg38_cpgs_subset        hg38_cpgs_subset
kallistoIndex           Create an index file for running Kallisto
kallistoQuantify        Run kallisto on a set of FASTQ files and merge
                        the results
liftoverMethRSE         Liftover rowRanges of a
                        RangedSummarizedExperiment for methylation data
                        from one genome build to another
maskRangesInRSE         Mask regions in a ranged summarized experiment
methodical-package      methodical: A one-stop shop for dealing with
                        big DNA methylation datasets
plotMethSiteCorCoefs    Plot the correlation coefficients for
                        methylation sites within a region and an
                        associated feature of interest
plotMethodicalScores    Create plot of Methodical score values for
                        methylation sites around a TSS
plotRegionValues        Create a scatter plot with smoothed curve for
                        values along adjacent loci in a genomic region
plotTMRs                Add TMRs to a methylation site value plot
rangesRelativeToTSS     Find locations of genomic regions relative to
                        transcription start sites.
rapidCorTest            Rapidly calculate the correlation and the
                        significance of pairs of columns from two
                        data.frames
sampleMethSites         Randomly sample sites from a methylation RSE.
strandedDistance        Calculate distances of query GRanges upstream
                        or downstream of subject GRanges
sumTranscriptValuesForGenes
                        Combine the expression values of transcripts to
                        get overall expression of their associated
                        genes
summarizeRegionMethylation
                        Summarize methylation of genomic regions within
                        samples
tubb6_correlation_plot
                        tubb6_correlation_plot
tubb6_cpg_meth_transcript_cors
                        tubb6_cpg_meth_transcript_cors
tubb6_meth_rse          tubb6_meth_rse
tubb6_tmrs              tubb6_tmrs
tubb6_transcript_counts
                        tubb6_transcript_counts
tubb6_tss               tubb6_tss
