COSMIC3.0_ID            Indel reference signatures for COSMIC3.0
COSMIC3.0_SBS           Single base substitution reference signatures
                        for COSMIC3.0
COSMIC3.1_CN            Copy Number reference signatures for COSMIC3.1
COSMIC3.3.1_SBS         Single base substitution reference signatures
                        for COSMIC3.3.1
COSMIC3.3.1_SBS_mm10    Mice Single base substitution reference
                        signatures for COSMIC3.3.1
COSMIC3.3_CN            Copy Number reference signatures for COSMIC3.3
COSMIC3.3_DBS           Double base reference signatures for COSMIC3.0
COSMIC3.3_DBS_mm10      Mice Double base reference signatures for
                        COSMIC3.0
COSMIC3.3_ID            Indel reference signatures for COSMIC3.3.1
EGFR_context_counts_ordered
                        Counts of each context class for the main
                        transcript of gene EGFR
EGFR_drivers_intogen_SBS96
                        SBS96 spectrum from the intogen website for
                        gene EGFR in lung adenocarcinomas
ESCC_countries_SBS      Single base substitution signature attributions
                        found in esophageal squamous cell carcinoma
                        across countries with varying incidence.
ESCC_countries_SBS.refs
                        Reference COSMIC Single base substitution
                        signatures found in esophageal squamous cell
                        carcinoma across countries with varying
                        incidence.
ESCC_sig_activity       Activity of SBS, DBS, and ID mutational
                        signatures in a global sample of esophageal
                        squamous cell carcinoma cases.
ESCC_sig_similarity     Cosine similarity of SBS, DBS, and ID
                        mutational signatures found in a global sample
                        of esophageal squamous cell carcinoma cases.
Intogen_EGFR_LUAD       Driver mutations from the intogen website for
                        gene EGFR in lung adenocarcinomas
MESOMICS_CN_SBS         Copy Number and Single Base Substitution
                        mutational signatures for 120 malignant pleural
                        mesothelioma from the MESOMICS cohort
PCAWG_SigProfiler_COSMIC_DBS
                        Double Base Substitution COSMIC mutational
                        signatures for 2780 tumors
PCAWG_SigProfiler_COSMIC_ID
                        Indel COSMIC mutational signatures for 2780
                        tumors
PCAWG_SigProfiler_COSMIC_SBS
                        Single Base Substitution COSMIC mutational
                        signatures for 2780 tumors
Sherlock_LCINS.metadata
                        Metadata accompanying mutational signatures for
                        lung cancer in never smokers.
Sherlock_LCINS_SBS      Single base substitution signature attributions
                        found in Lung cancer in never smokers.
Sherlock_LCINS_SBS.refs
                        Reference COSMIC Single base substitution
                        signatures found in Lung cancer in never
                        smokers.
TP53_context_counts_ordered
                        Counts of each context class for the main
                        transcript of gene TP53
TP53_drivers_intogen_LUAD
                        Driver mutations from the intogen website for
                        gene TP53 in lung adenocarcinomas
TP53_drivers_intogen_SBS96
                        SBS96 spectrum from the intogen website for
                        gene TP53 in lung adenocarcinomas
all_sig_pal             Color palette for mutational signatures
                        analyzed in the study by Morrison et al.
carcinogens_mice_SBS    Single base substitution signature attributions
                        found in mice exposed to 20 known or suspected
                        carcinogens.
carcinogens_mice_SBS.refs
                        Reference single base substitution signatures
                        found in mice exposed to 20 known or suspected
                        carcinogens.
cossim                  Compute the cosine similarity matrix for a set
                        of mutational signatures.
fst                     Compute the Fst of a matrix of compositional
                        vectors
fst_norm                Compute the normalized Fst of a matrix of
                        compositional vectors
get_SBS96_driver_spectrum
                        get_SBS96_driver_spectrum
get_SBS96_spectrum      get_SBS96_spectrum
het                     Compute the Gini-Simpson index of a
                        compositional vector
het_mean                Compute the mean Gini-Simpson index of the rows
                        in a matrix of compositional vectors
het_pooled              Compute the pooled Gini-Simpson index of the
                        rows in a matrix of compositional vectors
import_SigProfiler      import_SigProfiler
mutsig_carcinogens_mice_SBS
                        Single Base Substitution mutational signatures
                        for 181 mice exposed to known or suspected
                        carcinogens
mutsig_carcinogens_mice_SBS.refs
                        Definitions of murine single base substitution
                        mutational signatures
mutsig_carcinogens_mice_bootstrap_p_vals
                        Bootstrap p-values comparing SVA results for
                        carcinogen-exposed murine tumors to spontaneous
                        tumors
plot_SBS_spectrum       Plot an SBS mutational spectrum
plot_dots               Plot the mean mutational signature activities
                        of each group of samples
plot_signature_prop     Visualize a relative abundance matrix as a
                        stacked bar plot.
radiation_sigs_morton   Single base substitution signature attributions
                        found in papillary thyroid carcinoma from
                        Chernobyl incident survivors.
radiation_sigs_morton_cossim
                        Cosine similarity matrix of Single base
                        substitution signatures found in papillary
                        thyroid carcinoma from Chernobyl incident
                        survivors.
rcc_sig_activity        Activity of SBS, DBS, and ID mutational
                        signatures in a global sample of renal cell
                        carcinoma cases.
rcc_sim                 Activity of SBS, DBS, and ID mutational
                        signatures in a global sample of renal cell
                        carcinoma cases.
sbs_palette             Single Base Substitution COSMIC mutational
                        signatures for 2780 tumors
sigboot                 Statistically compare the within-sample
                        diversity and across-sample heterogeneity of
                        the mutational signature activity in two or
                        more groups of tumor samples.
sigvar                  Compute the within-sample diversity and
                        across-sample heterogeneity of mutational
                        signature activity in one or multiple
                        populations of samples.
smoker_sigs_chen        Activity of Smoking, APOBEC, and Ageing
                        mutational signatures in a sample of East Asian
                        lung adenocarcinoma patients.
smoker_sigs_chen_cossim
                        Cosine similarity of smoking, APOBEC, and
                        ageing mutational signatures found in a sample
                        of East Asian lung adenocarcinoma patients.
time_weights            Compute a normalized weighting vector based on
                        a vector of sampling times.
zhang_sig_activity      Activity of SBS mutational signatures in
                        samples of lung cancer in never smokers
zhang_sig_similarity    Cosine similarity of SBS mutational signatures
                        found in samples of lung cancer in never
                        smokers
