%>%	pipe
.jsd	dot-jsd
add_flank_to_variants	add_flank_to_variants
add_result	add_result
add_variant_type	add_variant_type
annotate_replication_strand	annotate_replication_strand
annotate_transcript_strand	annotate_transcript_strand
annotate_variant_length	annotate_variant_length
annotate_variant_type	annotate_variant_type
auto_predict_grid	auto_predict_grid
auto_subset_sigs	auto_subset_sigs
build_custom_table	build_custom_table
build_standard_table	build_standard_table
built_tables	built_tables
built_tables,musica-method	built_tables
cluster_exposure	cluster_exposure
combine_count_tables	combine_count_tables
combine_predict_grid	combine_predict_grid
compare_cosmic_v2	compare_cosmic_v2
compare_cosmic_v3	compare_cosmic_v3
compare_k_vals	compare_k_vals
compare_results	compare_results
cosmic_v2_sigs	cosmic_v2_sigs
cosmic_v2_subtype_map	cosmic_v2_subtype_map
cosmic_v3_dbs_sigs	cosmic_v3_dbs_sigs
cosmic_v3_indel_sigs	cosmic_v3_indel_sigs
cosmic_v3_sbs_sigs	cosmic_v3_sbs_sigs
cosmic_v3_sbs_sigs_exome	cosmic_v3_sbs_sigs_exome
count_table-class	count_table-class
create_dbs78_table	create_dbs78_table
create_musica_from_counts	create_musica_from_counts
create_musica_from_variants	create_musica_from_variants
create_sbs192_table	create_sbs192_table
create_sbs96_table	create_sbs96_table
create_umap	create_umap
credible_intervals	credible_intervals
credible_intervals,musica-method	credible_intervals
credible_intervals,result_collection-method	credible_intervals
credible_intervals,result_model-method	credible_intervals
credible_intervals<-	credible_intervals
credible_intervals<-,musica,matrix-method	credible_intervals
credible_intervals<-,result_collection,matrix-method	credible_intervals
credible_intervals<-,result_model,matrix-method	credible_intervals
dbs_musica	dbs_musica
discover_signatures	discover_signatures
drop_annotation	drop_annotation
exposures	exposures
exposures,musica-method	exposures
exposures,result_collection-method	exposures
exposures,result_model-method	exposures
exposures<-	exposures
exposures<-,musica,matrix-method	exposures
exposures<-,result_collection,matrix-method	exposures
exposures<-,result_model,matrix-method	exposures
exposure_differential_analysis	exposure_differential_analysis
extract_count_tables	extract_count_tables
extract_variants	extract_variants
extract_variants_from_maf	extract_variants_from_maf
extract_variants_from_maf_file	extract_variants_from_maf_file
extract_variants_from_matrix	extract_variants_from_matrix
extract_variants_from_vcf	extract_variants_from_vcf
extract_variants_from_vcf_file	extract_variants_from_vcf_file
generate_result_grid	generate_result_grid
get_count_table	get_count_table
get_modality	get_modality
get_modality,musica-method	get_modality
get_modality,result_collection-method	get_modality
get_model	get_model
get_model,musica-method	get_model
get_model,result_collection-method	get_model
get_result_list_entry	get_result_list_entry
get_result_list_entry,musica,character-method	get_result_list_entry
hyperparameter	hyperparameter
hyperparameter,musica-method	hyperparameter
hyperparameter,result_collection-method	hyperparameter
hyperparameter<-	hyperparameter
hyperparameter<-,musica,list-method	hyperparameter
hyperparameter<-,result_collection,list-method	hyperparameter
indel_musica	indel_musica
k_select	k_select
metrics	metrics
metrics,musica-method	metrics
metrics,result_collection-method	metrics
metrics,result_model-method	metrics
metrics<-	metrics
metrics<-,musica,SimpleList-method	metrics
metrics<-,result_collection,SimpleList-method	metrics
metrics<-,result_model,SimpleList-method	metrics
modality	modality
modality,musica-method	modality
modality,result_collection-method	modality
modality,result_model-method	modality
modality<-	modality
modality<-,musica,matrix-method	modality
modality<-,result_collection,matrix-method	modality
modality<-,result_model,matrix-method	modality
model_id	model_id
model_id,musica-method	model_id
model_id,result_collection-method	model_id
model_id,result_model-method	model_id
model_id<-	model_id
model_id<-,musica,matrix-method	model_id
model_id<-,result_collection,matrix-method	model_id
model_id<-,result_model,matrix-method	model_id
musica	musica
musica-class	musica-class
musicatk	musicatk
musica_annot	musica_annot
musica_sbs96	musica_sbs96
musica_sbs96_tiny	musica_sbs96_tiny
name_signatures	name_signatures
num_signatures	num_signatures
num_signatures,musica-method	num_signatures
num_signatures,result_collection-method	num_signatures
num_signatures,result_model-method	num_signatures
num_signatures<-	num_signatures
num_signatures<-,musica,matrix-method	num_signatures
num_signatures<-,result_collection,matrix-method	num_signatures
num_signatures<-,result_model,matrix-method	num_signatures
other_parameters	other_parameters
other_parameters,musica-method	other_parameters
other_parameters,result_collection-method	other_parameters
other_parameters,result_model-method	other_parameters
other_parameters<-	other_parameters
other_parameters<-,musica,matrix-method	other_parameters
other_parameters<-,result_collection,matrix-method	other_parameters
other_parameters<-,result_model,matrix-method	other_parameters
parameter	parameter
parameter,musica-method	parameter
parameter,result_collection-method	parameter
parameter<-	parameter
parameter<-,musica,list-method	parameter
parameter<-,result_collection,list-method	parameter
plot_cluster	plot_cluster
plot_differential_analysis	plot_differential_analysis
plot_exposures	plot_exposures
plot_heatmap	plot_heatmap
plot_k_comparison	plot_k_comparison
plot_sample_counts	plot_sample_counts
plot_sample_reconstruction_error	plot_sample_reconstruction_error
plot_signatures	plot_signatures
plot_umap	plot_umap
predict_exposure	predict_exposure
rc	rc
rep_range	rep_range
res	res
result_collection-class	result_collection-class
result_list	result_list
result_list,musica-method	result_list
result_list<-	result_list
result_list<-,musica,SimpleList-method	result_list
result_model-class	result_model-class
res_annot	res_annot
sample_names	sample_names
sample_names,musica-method	sample_names
samp_annot	samp_annot
samp_annot,musica-method	samp_annot
samp_annot<-	samp_annot
samp_annot<-,musica,character,vector-method	samp_annot
select_genome	select_genome
signatures	signatures
signatures,musica-method	signatures
signatures,result_collection-method	signatures
signatures,result_model-method	signatures
signatures<-	signatures
signatures<-,musica,matrix-method	signatures
signatures<-,result_collection,matrix-method	signatures
signatures<-,result_model,matrix-method	signatures
subset_musica_by_annotation	subset_musica_by_annotation
subset_musica_by_counts	subset_musica_by_counts
subset_variants_by_samples	subset_variants_by_samples
subset_variant_by_type	subset_variant_by_type
tables	tables
tables,musica-method	tables
tables<-	tables
tables<-,musica,list-method	tables
table_96	table_96
table_selected	table_selected
table_selected,result_model-method	table_selected
umap	umap
umap,musica-method	umap
umap,result_collection-method	umap
umap,result_model-method	umap
umap<-	umap
umap<-,musica,matrix-method	umap
umap<-,result_collection,matrix-method	umap
umap<-,result_model,matrix-method	umap
variants	variants
variants,musica-method	variants
variants<-	variants
variants<-,musica,data.table-method	variants
