add_annotation	add_annotation
add_as_fist_to_list	add_as_fist_to_list
aggregate_exposures_by_category	aggregate_exposures_by_category
AlexCosmicArtif_sigInd_df	sigs
AlexCosmicArtif_sig_df	sigs
AlexCosmicValid_sigInd_df	sigs
AlexCosmicValid_sig_df	sigs
AlexInitialArtif_sigInd_df	sigs
AlexInitialArtif_sig_df	sigs
AlexInitialValid_sigInd_df	sigs
AlexInitialValid_sig_df	sigs
annotate_intermut_dist_cohort	annotate_intermut_dist_cohort
annotate_intermut_dist_PID	annotate_intermut_dist_PID
annotation_exposures_barplot	annotation_exposures_barplot
annotation_exposures_list_barplot	annotation_exposures_list_barplot
annotation_heatmap_exposures	annotation_heatmap_exposures
attribute_nucleotide_exchanges	attribute_nucleotide_exchanges
attribute_sequence_contex_indel	attribute_sequence_contex_indel
attribution_of_indels	attribution_of_indels
average_over_present	normalize_df_per_dim
build_gene_list_for_pathway	build_gene_list_for_pathway
chosen_AlexInitialArtif_sigInd_df	exampleYAPSA
chosen_signatures_indices_df	exampleYAPSA
classify_indels	classify_indels
compare_exposures	compare_exposures
compare_expousre_sets	compare_expousre_sets
compare_sets	compare_sets
compare_SMCs	compare_SMCs
compare_to_catalogues	compare_to_catalogues
complex_heatmap_exposures	complex_heatmap_exposures
computeLogLik	computeLogLik
compute_comparison_stat_df	compute_comparison_stat_df
confidence_indel_calulation	confidence_indel_calulation
confidence_indel_only_calulation	confidence_indel_only_calulation
confIntExp	confIntExp
correct_rounded	correct_rounded
cosineDist	cosineDist
cosineMatchDist	cosineMatchDist
COSMIC_subgroups_df	exampleYAPSA
create_indel_mutation_catalogue_from_df	create_indel_mutation_catalogue_from_df
create_indel_mut_cat_from_df	create_indel_mut_cat_from_df
create_mutation_catalogue_from_df	create_mutation_catalogue_from_df
create_mutation_catalogue_from_VR	create_mutation_catalogue_from_VR
cutoffCosmicArtif_abs_df	cutoffs
cutoffCosmicArtif_rel_df	cutoffs
cutoffCosmicValid_abs_df	cutoffs
cutoffCosmicValid_rel_df	cutoffs
cutoffInitialArtif_abs_df	cutoffs
cutoffInitialArtif_rel_df	cutoffs
cutoffInitialValid_abs_df	cutoffs
cutoffInitialValid_rel_df	cutoffs
cutoffPCAWG_ID_WGS_Pid_df	cutoffs_pcawg
cutoffPCAWG_SBS_WGSWES_artifPid_df	cutoffs_pcawg
cutoffPCAWG_SBS_WGSWES_realPid_df	cutoffs_pcawg
cutoffs	cutoffs
cutoffs_pcawg	cutoffs_pcawg
cut_breaks_as_intervals	cut_breaks_as_intervals
deriveSigInd_df	deriveSigInd_df
disambiguateVector	disambiguateVector
enrichSigs	enrichSigs
exampleINDEL_YAPSA	exampleINDEL_YAPSA
exampleYAPSA	exampleYAPSA
exchange_colour_vector	exchange_colour_vector
exome_mutCatRaw_df	exome_mutCatRaw_df
exposures_barplot	exposures_barplot
extract_names_from_gene_list	extract_names_from_gene_list
find_affected_PIDs	find_affected_PIDs
GenomeOfNl_raw	GenomeOfNl_raw
getSequenceContext	getSequenceContext
get_extreme_PIDs	get_extreme_PIDs
hclust_exposures	hclust_exposures
LCD	LCD
LCD_complex_cutoff	LCD_complex_cutoff
LCD_complex_cutoff_combined	LCD_complex_cutoff
LCD_complex_cutoff_consensus	LCD_complex_cutoff
LCD_complex_cutoff_perPID	LCD_complex_cutoff
LCD_extractCohort_callPerPID	LCD_complex_cutoff
LCD_SMC	LCD_SMC
logLikelihood	logLikelihood
lymphomaNature2013_mutCat_df	lymphomaNature2013_mutCat_df
lymphoma_Nature2013_COSMIC_cutoff_exposures_df	exampleYAPSA
lymphoma_Nature2013_raw_df	exampleYAPSA
lymphoma_PID_df	exampleYAPSA
lymphoma_test_df	exampleYAPSA
makeVRangesFromDataFrame	makeVRangesFromDataFrame
make_catalogue_strata_df	make_catalogue_strata_df
make_comparison_matrix	make_comparison_matrix
make_strata_df	make_strata_df
make_subgroups_df	make_subgroups_df
melt_exposures	melt_exposures
merge_exposures	merge_exposures
MutCat_indel_df	MutCat_indel_df
normalizeMotifs_otherRownames	normalizeMotifs_otherRownames
normalize_df_per_dim	normalize_df_per_dim
PCAWG_SP_ID_sigInd_df	sigs_pcawg
PCAWG_SP_ID_sigs_df	sigs_pcawg
PCAWG_SP_SBS_sigInd_Artif_df	sigs_pcawg
PCAWG_SP_SBS_sigInd_Real_df	sigs_pcawg
PCAWG_SP_SBS_sigs_Artif_df	sigs_pcawg
PCAWG_SP_SBS_sigs_Real_df	sigs_pcawg
plotExchangeSpectra	plotExchangeSpectra
plotExchangeSpectra_indel	plotExchangeSpectra_indel
plotExposuresConfidence	plotExposuresConfidence
plotExposuresConfidence_indel	plotExposuresConfidence_indel
plot_exposures	plot_exposures
plot_relative_exposures	plot_exposures
plot_SMC	plot_SMC
plot_strata	plot_strata
read_entry	read_entry
read_list	read_entry
relateSigs	relateSigs
rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df	exampleYAPSA
repeat_df	repeat_df
round_precision	round_precision
run_annotate_vcf_pl	run_annotate_vcf_pl
run_comparison_catalogues	run_comparison_catalogues
run_comparison_general	run_comparison_general
run_kmer_frequency_correction	run_kmer_frequency_correction
run_kmer_frequency_normalization	run_kmer_frequency_normalization
run_plot_strata_general	run_plot_strata_general
run_SMC	run_SMC
sd_over_present	normalize_df_per_dim
shapiro_if_possible	shapiro_if_possible
sigs	sigs
sigs_pcawg	sigs_pcawg
SMC	SMC
SMC_perPID	SMC_perPID
split_exposures_by_subgroups	split_exposures_by_subgroups
stat_plot_subgroups	stat_plot_subgroups
stat_test_SMC	stat_test_SMC
stat_test_subgroups	stat_test_subgroups
stderrmean	stderrmean
stderrmean_over_present	normalize_df_per_dim
sum_over_list_of_df	sum_over_list_of_df
targetCapture_cor_factors	targetCapture_cor_factors
testSigs	testSigs
test_exposureAffected	test_exposureAffected
test_gene_list_in_exposures	test_gene_list_in_exposures
transform_rownames_deconstructSigs_to_YAPSA	transform_rownames_R_to_MATLAB
transform_rownames_MATLAB_to_R	transform_rownames_R_to_MATLAB
transform_rownames_nature_to_R	transform_rownames_R_to_MATLAB
transform_rownames_R_to_MATLAB	transform_rownames_R_to_MATLAB
transform_rownames_YAPSA_to_deconstructSigs	transform_rownames_R_to_MATLAB
translate_to_1kG	translate_to_hg19
translate_to_hg19	translate_to_hg19
trellis_rainfall_plot	trellis_rainfall_plot
variateExp	variateExp
variateExpSingle	variateExpSingle
YAPSA	YAPSA
