├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── CHANGELOG ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── data.R ├── sigfit-package.R ├── sigfit_estimation.R ├── sigfit_plotting.R ├── sigfit_utility.R └── stanmodels.R ├── README.md ├── configure ├── configure.win ├── data ├── cosmic_signatures_doublet_v3.2.RData ├── cosmic_signatures_indel_v3.2.RData ├── cosmic_signatures_strand_v3.RData ├── cosmic_signatures_v2.RData ├── cosmic_signatures_v3.2.RData ├── cosmic_signatures_v3.RData ├── counts_119breast.RData ├── counts_119breast_strand.RData ├── counts_21breast.RData ├── counts_88liver.RData ├── counts_88liver_strand.RData ├── methylation_27normal.RData ├── methylation_50breast.RData ├── sigfit_vignette_data.RData ├── variants_119breast.RData ├── variants_119breast_strand.RData ├── variants_21breast.RData ├── variants_88liver.RData └── variants_88liver_strand.RData ├── doc ├── sigfit_vignette.R ├── sigfit_vignette.Rmd └── sigfit_vignette.html ├── inst ├── CITATION ├── include │ └── stan_meta_header.hpp └── stan │ ├── include │ ├── common_functions.stan │ └── license.stan │ ├── sigfit_ext.stan │ ├── sigfit_fit.stan │ └── sigfit_fitext.stan ├── logo.png ├── man ├── build_catalogues.Rd ├── build_opps_matrix.Rd ├── calculate_gof.Rd ├── convert_signatures.Rd ├── cosine_sim.Rd ├── cosmic_signatures_doublet_v3.2.Rd ├── cosmic_signatures_indel_v3.2.Rd ├── cosmic_signatures_strand_v3.Rd ├── cosmic_signatures_v2.Rd ├── cosmic_signatures_v3.2.Rd ├── cosmic_signatures_v3.Rd ├── default_sig_palette.Rd ├── extract_signatures.Rd ├── extract_signatures_initialiser.Rd ├── fetch_cosmic_data.Rd ├── fit_extract_signatures.Rd ├── fit_signatures.Rd ├── get_initializer_list.Rd ├── get_loglik.Rd ├── get_reconstructions.Rd ├── human_trinuc_freqs.Rd ├── l2_norm.Rd ├── letterwrap.Rd ├── make_colors.Rd ├── match_signatures.Rd ├── mut_types.Rd ├── plot_all.Rd ├── plot_exposures.Rd ├── plot_gof.Rd ├── plot_ppc.Rd ├── plot_reconstruction.Rd ├── plot_spectrum.Rd ├── plot_spectrum_dbs.Rd ├── plot_spectrum_generic.Rd ├── plot_spectrum_id.Rd ├── plot_spectrum_sbs.Rd ├── plot_spectrum_tsw.Rd ├── remove_zeros_.Rd ├── retrieve_pars.Rd ├── rev_comp.Rd ├── sigfit-package.Rd ├── simulate_ppc.Rd ├── stan_models.Rd └── to_matrix.Rd ├── src ├── Makevars └── Makevars.win └── vignettes └── sigfit_vignette.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/.travis.yml -------------------------------------------------------------------------------- /CHANGELOG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/CHANGELOG -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/LICENSE -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/R/data.R -------------------------------------------------------------------------------- /R/sigfit-package.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/R/sigfit-package.R -------------------------------------------------------------------------------- /R/sigfit_estimation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/R/sigfit_estimation.R -------------------------------------------------------------------------------- /R/sigfit_plotting.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/R/sigfit_plotting.R -------------------------------------------------------------------------------- /R/sigfit_utility.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/R/sigfit_utility.R -------------------------------------------------------------------------------- /R/stanmodels.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/R/stanmodels.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/README.md -------------------------------------------------------------------------------- /configure: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/configure -------------------------------------------------------------------------------- /configure.win: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/configure.win -------------------------------------------------------------------------------- /data/cosmic_signatures_doublet_v3.2.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/cosmic_signatures_doublet_v3.2.RData -------------------------------------------------------------------------------- /data/cosmic_signatures_indel_v3.2.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/cosmic_signatures_indel_v3.2.RData -------------------------------------------------------------------------------- /data/cosmic_signatures_strand_v3.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/cosmic_signatures_strand_v3.RData -------------------------------------------------------------------------------- /data/cosmic_signatures_v2.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/cosmic_signatures_v2.RData -------------------------------------------------------------------------------- /data/cosmic_signatures_v3.2.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/cosmic_signatures_v3.2.RData -------------------------------------------------------------------------------- /data/cosmic_signatures_v3.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/cosmic_signatures_v3.RData -------------------------------------------------------------------------------- /data/counts_119breast.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/counts_119breast.RData -------------------------------------------------------------------------------- /data/counts_119breast_strand.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/counts_119breast_strand.RData -------------------------------------------------------------------------------- /data/counts_21breast.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/counts_21breast.RData -------------------------------------------------------------------------------- /data/counts_88liver.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/counts_88liver.RData -------------------------------------------------------------------------------- /data/counts_88liver_strand.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/counts_88liver_strand.RData -------------------------------------------------------------------------------- /data/methylation_27normal.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/methylation_27normal.RData -------------------------------------------------------------------------------- /data/methylation_50breast.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/methylation_50breast.RData -------------------------------------------------------------------------------- /data/sigfit_vignette_data.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/sigfit_vignette_data.RData -------------------------------------------------------------------------------- /data/variants_119breast.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/variants_119breast.RData -------------------------------------------------------------------------------- /data/variants_119breast_strand.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/variants_119breast_strand.RData -------------------------------------------------------------------------------- /data/variants_21breast.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/variants_21breast.RData -------------------------------------------------------------------------------- /data/variants_88liver.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/variants_88liver.RData -------------------------------------------------------------------------------- /data/variants_88liver_strand.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/data/variants_88liver_strand.RData -------------------------------------------------------------------------------- /doc/sigfit_vignette.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/doc/sigfit_vignette.R -------------------------------------------------------------------------------- /doc/sigfit_vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/doc/sigfit_vignette.Rmd -------------------------------------------------------------------------------- /doc/sigfit_vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/doc/sigfit_vignette.html -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/include/stan_meta_header.hpp: -------------------------------------------------------------------------------- 1 | // Insert all #include statements here 2 | -------------------------------------------------------------------------------- /inst/stan/include/common_functions.stan: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/inst/stan/include/common_functions.stan -------------------------------------------------------------------------------- /inst/stan/include/license.stan: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/inst/stan/include/license.stan -------------------------------------------------------------------------------- /inst/stan/sigfit_ext.stan: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/inst/stan/sigfit_ext.stan -------------------------------------------------------------------------------- /inst/stan/sigfit_fit.stan: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/inst/stan/sigfit_fit.stan -------------------------------------------------------------------------------- /inst/stan/sigfit_fitext.stan: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/inst/stan/sigfit_fitext.stan -------------------------------------------------------------------------------- /logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/logo.png -------------------------------------------------------------------------------- /man/build_catalogues.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/build_catalogues.Rd -------------------------------------------------------------------------------- /man/build_opps_matrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/build_opps_matrix.Rd -------------------------------------------------------------------------------- /man/calculate_gof.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/calculate_gof.Rd -------------------------------------------------------------------------------- /man/convert_signatures.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/convert_signatures.Rd -------------------------------------------------------------------------------- /man/cosine_sim.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/cosine_sim.Rd -------------------------------------------------------------------------------- /man/cosmic_signatures_doublet_v3.2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/cosmic_signatures_doublet_v3.2.Rd -------------------------------------------------------------------------------- /man/cosmic_signatures_indel_v3.2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/cosmic_signatures_indel_v3.2.Rd -------------------------------------------------------------------------------- /man/cosmic_signatures_strand_v3.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/cosmic_signatures_strand_v3.Rd -------------------------------------------------------------------------------- /man/cosmic_signatures_v2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/cosmic_signatures_v2.Rd -------------------------------------------------------------------------------- /man/cosmic_signatures_v3.2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/cosmic_signatures_v3.2.Rd -------------------------------------------------------------------------------- /man/cosmic_signatures_v3.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/cosmic_signatures_v3.Rd -------------------------------------------------------------------------------- /man/default_sig_palette.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/default_sig_palette.Rd -------------------------------------------------------------------------------- /man/extract_signatures.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/extract_signatures.Rd -------------------------------------------------------------------------------- /man/extract_signatures_initialiser.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/extract_signatures_initialiser.Rd -------------------------------------------------------------------------------- /man/fetch_cosmic_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/fetch_cosmic_data.Rd -------------------------------------------------------------------------------- /man/fit_extract_signatures.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/fit_extract_signatures.Rd -------------------------------------------------------------------------------- /man/fit_signatures.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/fit_signatures.Rd -------------------------------------------------------------------------------- /man/get_initializer_list.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/get_initializer_list.Rd -------------------------------------------------------------------------------- /man/get_loglik.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/get_loglik.Rd -------------------------------------------------------------------------------- /man/get_reconstructions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/get_reconstructions.Rd -------------------------------------------------------------------------------- /man/human_trinuc_freqs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/human_trinuc_freqs.Rd -------------------------------------------------------------------------------- /man/l2_norm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/l2_norm.Rd -------------------------------------------------------------------------------- /man/letterwrap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/letterwrap.Rd -------------------------------------------------------------------------------- /man/make_colors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/make_colors.Rd -------------------------------------------------------------------------------- /man/match_signatures.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/match_signatures.Rd -------------------------------------------------------------------------------- /man/mut_types.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/mut_types.Rd -------------------------------------------------------------------------------- /man/plot_all.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_all.Rd -------------------------------------------------------------------------------- /man/plot_exposures.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_exposures.Rd -------------------------------------------------------------------------------- /man/plot_gof.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_gof.Rd -------------------------------------------------------------------------------- /man/plot_ppc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_ppc.Rd -------------------------------------------------------------------------------- /man/plot_reconstruction.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_reconstruction.Rd -------------------------------------------------------------------------------- /man/plot_spectrum.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_spectrum.Rd -------------------------------------------------------------------------------- /man/plot_spectrum_dbs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_spectrum_dbs.Rd -------------------------------------------------------------------------------- /man/plot_spectrum_generic.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_spectrum_generic.Rd -------------------------------------------------------------------------------- /man/plot_spectrum_id.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_spectrum_id.Rd -------------------------------------------------------------------------------- /man/plot_spectrum_sbs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_spectrum_sbs.Rd -------------------------------------------------------------------------------- /man/plot_spectrum_tsw.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/plot_spectrum_tsw.Rd -------------------------------------------------------------------------------- /man/remove_zeros_.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/remove_zeros_.Rd -------------------------------------------------------------------------------- /man/retrieve_pars.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/retrieve_pars.Rd -------------------------------------------------------------------------------- /man/rev_comp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/rev_comp.Rd -------------------------------------------------------------------------------- /man/sigfit-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/sigfit-package.Rd -------------------------------------------------------------------------------- /man/simulate_ppc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/simulate_ppc.Rd -------------------------------------------------------------------------------- /man/stan_models.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/stan_models.Rd -------------------------------------------------------------------------------- /man/to_matrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/man/to_matrix.Rd -------------------------------------------------------------------------------- /src/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/src/Makevars -------------------------------------------------------------------------------- /src/Makevars.win: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/src/Makevars.win -------------------------------------------------------------------------------- /vignettes/sigfit_vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kgori/sigfit/HEAD/vignettes/sigfit_vignette.Rmd --------------------------------------------------------------------------------