| add_frag_info | decode fragment identifiers for spike-in standards |
| bam_to_bins | create a tiled representation of a genome from the BAM/CRAM... |
| bin_pmol | Binned estimation of picomoles of DNA present in cfMeDIP... |
| convertPairedGRtoGR | Convert Pairs to GRanges |
| covg_to_df | reshape 'scan_spiked_bam' results into data.frames for... |
| dedup | spike-in counts for two samples, as a wide data.frame |
| find_spike_contigs | find spike-in seqlevels in an object 'x', where... |
| genbank_mito | various mitochondrial genomes sometimes used as endogenous... |
| generate_spike_fasta | for CRAM files, a FASTA reference is required to decode; this... |
| genomic_res | A Granges object with genomic coverage from chr21q22, binned... |
| 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... |
| get_spiked_coverage | tabulate coverage across assembly and spike contig subset in... |
| get_spike_depth | get the (max, median, or mean) coverage for spike-in contigs... |
| kmax | simple contig kmer comparisons |
| kmers | oligonucleotideFrequency, but less letters and more... |
| methylation_specificity | compute methylation specificity for spike-in standards |
| model_bam_standards | Build a Bayesian additive model from spike-ins to correct... |
| model_glm_pmol | Build a generalized linear model from spike-ins to correct... |
| parse_spike_UMI | parse out the forward and reverse UMIs and contig for a... |
| phage | lambda and phiX phage sequences, sometimes used as spike-ins |
| predict_pmol | predict picomoles of DNA from a fit and read counts... |
| process_spikes | QC, QA, and processing for a new spike database |
| read_bedpe | read a BEDPE file into Pairs of GRanges (as if a... |
| rename_spikes | for BAM/CRAM files with renamed contigs, we need to rename... |
| rename_spike_seqlevels | for spike-in contigs in GRanges, match to standardized spike... |
| scan_genomic_bedpe | Scan genomic BEDPE |
| scan_genomic_contigs | scan genomic contigs in a BAM/CRAM file |
| scan_methylation_specificity | tabulate methylation specificity for multiple spike-in... |
| scan_spike_bedpe | Scan spikes BEDPE |
| scan_spike_contigs | pretty much what it says: scan spike contigs from a BAM or... |
| scan_spike_counts | run spike_counts on BAM/CRAM files and shape the results for... |
| scan_spiked_bam | pretty much what it says: scan standard chroms + spike... |
| seqinfo_from_header | create seqinfo (and thus a standard chromosome filter) from a... |
| 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... |
| spike_cram_counts | spike-in counts, as a long data.frame |
| spike_read_counts | spike-in counts, as a long data.frame |
| spike_res | A Granges object with spike-in sequence coverage, and... |
| 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... |
| testGR | a test GRanges with UMI'ed genomic sequences used as controls |
| tile_bins | Tile the assembly-based contigs of a merged assembly/spike... |
