add_frag_info	add_frag_info
bam_to_bins	bam_to_bins
bin_pmol	bin_pmol
convertPairedGRtoGR	convertPairedGRtoGR
covg_to_df	covg_to_df
dedup	dedup
find_spike_contigs	find_spike_contigs
genbank_mito	genbank_mito
generate_spike_fasta	generate_spike_fasta
genomic_res	genomic_res
get_base_name	get_base_name
get_binned_coverage	get_binned_coverage
get_merged_gr	get_merged_gr
get_spiked_coverage	get_spiked_coverage
get_spike_depth	get_spike_depth
kmax	kmax
kmers	kmers
methylation_specificity	methylation_specificity
model_bam_standards	model_bam_standards
model_glm_pmol	model_glm_pmol
parse_spike_UMI	parse_spike_UMI
phage	phage
plot,Rle,ANY-method	spiky-methods
plot,SimpleRleList,ANY-method	spiky-methods
predict_pmol	predict_pmol
process_spikes	process_spikes
read_bedpe	read_bedpe
rename_spikes	rename_spikes
rename_spike_seqlevels	rename_spike_seqlevels
scan_genomic_bedpe	scan_genomic_bedpe
scan_genomic_contigs	scan_genomic_contigs
scan_methylation_specificity	scan_methylation_specificity
scan_spiked_bam	scan_spiked_bam
scan_spike_bedpe	scan_spike_bedpe
scan_spike_contigs	scan_spike_contigs
scan_spike_counts	scan_spike_counts
seqinfo_from_header	seqinfo_from_header
spike	spike
spike_bland_altman_plot	spike_bland_altman_plot
spike_counts	spike_counts
spike_cram_counts	spike_cram_counts
spike_read_counts	spike_read_counts
spike_res	spike_res
spiky-methods	spiky-methods
ssb_res	ssb_res
testGR	testGR
tile_bins	tile_bins
