MutationalPatterns-package	MutationalPatterns-package
binomial_test	binomial_test
bin_mutation_density	bin_mutation_density
calculate_lesion_segregation	calculate_lesion_segregation
cluster_signatures	cluster_signatures
context_potential_damage_analysis	context_potential_damage_analysis
convert_sigs_to_ref	convert_sigs_to_ref
cos_sim	cos_sim
cos_sim_matrix	cos_sim_matrix
count_dbs_contexts	count_dbs_contexts
count_indel_contexts	count_indel_contexts
count_mbs_contexts	count_mbs_contexts
enrichment_depletion_test	enrichment_depletion_test
explained_by_signatures	MutationalPatterns-defunct
extract_signatures	extract_signatures
fit_to_signatures	fit_to_signatures
fit_to_signatures_bootstrapped	fit_to_signatures_bootstrapped
fit_to_signatures_strict	fit_to_signatures_strict
genomic_distribution	genomic_distribution
get_dbs_context	get_dbs_context
get_indel_context	get_indel_context
get_known_signatures	get_known_signatures
get_mut_type	get_mut_type
lengthen_mut_matrix	lengthen_mut_matrix
merge_signatures	merge_signatures
MutationalPatterns	MutationalPatterns-package
mutations_from_vcf	mutations_from_vcf
mutation_context	MutationalPatterns-defunct
mutation_types	MutationalPatterns-defunct
mut_192_occurrences	mut_192_occurrences
mut_96_occurrences	mut_96_occurrences
mut_context	mut_context
mut_matrix	mut_matrix
mut_matrix_stranded	mut_matrix_stranded
mut_strand	mut_strand
mut_type	mut_type
mut_type_occurrences	mut_type_occurrences
plot_192_profile	plot_192_profile
plot_96_profile	plot_96_profile
plot_bootstrapped_contribution	plot_bootstrapped_contribution
plot_compare_dbs	plot_compare_dbs
plot_compare_indels	plot_compare_indels
plot_compare_mbs	plot_compare_mbs
plot_compare_profiles	plot_compare_profiles
plot_contribution	plot_contribution
plot_contribution_heatmap	plot_contribution_heatmap
plot_correlation_bootstrap	plot_correlation_bootstrap
plot_cosine_heatmap	plot_cosine_heatmap
plot_dbs_contexts	plot_dbs_contexts
plot_enrichment_depletion	plot_enrichment_depletion
plot_indel_contexts	plot_indel_contexts
plot_lesion_segregation	plot_lesion_segregation
plot_main_dbs_contexts	plot_main_dbs_contexts
plot_main_indel_contexts	plot_main_indel_contexts
plot_mbs_contexts	plot_mbs_contexts
plot_original_vs_reconstructed	plot_original_vs_reconstructed
plot_profile_heatmap	plot_profile_heatmap
plot_profile_region	plot_profile_region
plot_rainfall	plot_rainfall
plot_river	plot_river
plot_signature_strand_bias	plot_signature_strand_bias
plot_spectrum	plot_spectrum
plot_spectrum_region	plot_spectrum_region
plot_strand	plot_strand
plot_strand_bias	plot_strand_bias
pool_mut_mat	pool_mut_mat
read_vcfs_as_granges	read_vcfs_as_granges
rename_nmf_signatures	rename_nmf_signatures
signature_potential_damage_analysis	signature_potential_damage_analysis
split_muts_region	split_muts_region
strand_bias_test	strand_bias_test
strand_from_vcf	MutationalPatterns-defunct
strand_occurrences	strand_occurrences
type_context	type_context
