add_frag_info           decode fragment identifiers for spike-in
                        standards
bam_to_bins             create a tiled representation of a genome from
                        the BAM/CRAM file
bin_pmol                Binned estimation of picomoles of DNA present
                        in cfMeDIP assays
covg_to_df              reshape 'scan_spiked_bam' results into
                        data.frames for model_glm_pmol
dedup                   spike-in counts for two samples, as a wide
                        data.frame
find_spike_contigs      find spike-in seqlevels in an object 'x', where
                        !is.null(seqinfo(x))
genbank_mito            various mitochondrial genomes sometimes used as
                        endogenous spike-ins
generate_spike_fasta    for CRAM files, a FASTA reference is required
                        to decode; this builds that
get_base_name           refactored out of rename_spikes and
                        rename_spike_seqlevels
get_binned_coverage     tabulate read coverage in predefined bins
get_merged_gr           get a GRanges of (by default, standard)
                        chromosomes from seqinfo
get_spike_depth         get the (max, median, or mean) coverage for
                        spike-in contigs from a BAM/CRAM
get_spiked_coverage     tabulate coverage across assembly and spike
                        contig subset in natural order
kmax                    simple contig kmer comparisons
kmers                   oligonucleotideFrequency, but less letters and
                        more convenient.
methylation_specificity
                        compute methylation specificity for spike-in
                        standards
model_bam_standards     Build a Bayesian additive model from spike-ins
                        to correct bias in *-seq
model_glm_pmol          Build a generalized linear model from spike-ins
                        to correct bias in cfMeDIP
parse_spike_UMI         parse out the forward and reverse UMIs and
                        contig for a BED/BAM
phage                   lambda and phiX phage sequences, sometimes used
                        as spike-ins
predict_pmol            predict picomoles of DNA from a fit and read
                        counts (coverage)
process_spikes          QC, QA, and processing for a new spike database
rename_spike_seqlevels
                        for spike-in contigs in GRanges, match to
                        standardized spike seqlevels
rename_spikes           for BAM/CRAM files with renamed contigs, we
                        need to rename 'spike' rows
scan_genomic_contigs    scan genomic contigs in a BAM/CRAM file
scan_methylation_specificity
                        tabulate methylation specificity for multiple
                        spike-in BAM/CRAM files
scan_spike_contigs      pretty much what it says: scan spike contigs
                        from a BAM or CRAM file
scan_spike_counts       run spike_counts on BAM/CRAM files and shape
                        the results for model_glm_pmol
scan_spiked_bam         pretty much what it says: scan standard chroms
                        + spike contigs from a BAM
seqinfo_from_header     create seqinfo (and thus a standard chromosome
                        filter) from a BAM/CRAM header
spike                   spike-in contig properties for Sam's cfMeDIP
                        spikes
spike_bland_altman_plot
                        Bland-Altman plot for cfMeDIP spike standards
spike_counts            use the index of a spiked BAM/CRAM file for
                        spike contig coverage
spike_cram_counts       spike-in counts, as a long data.frame
spike_read_counts       spike-in counts, as a long data.frame
spiky-methods           A handful of methods that I've always felt were
                        missing
ssb_res                 scan_spiked_bam results from a merged cfMeDIP
                        CRAM file (chr22 and spikes)
testGR                  a test GRanges with UMI'ed genomic sequences
                        used as controls
tile_bins               Tile the assembly-based contigs of a merged
                        assembly/spike GRanges.
