Files in eyzhao/SignIT
What the Package Does (One Line, Title Case)
DESCRIPTION
NAMESPACE
R/SignIT-package.R
R/collapse_signatures_by_bleed.R
R/get_density_mode.R
R/get_exposure_pairwise_correlations.R
R/get_exposure_summary_table.R
R/get_exposures.R
R/get_mutation_types.R
R/get_os.R
R/get_population_signatures.R
R/get_populations.R
R/get_reference_signatures.R
R/get_signature_bleed_graph.R
R/get_signature_names.R
R/get_vaf_correction.R
R/mcmc_exposures_as_matrix.R
R/mutation_types_match.R
R/normalize_reference_signatures.R
R/parse_population_signatures.R
R/plot_bleed_interactions.R
R/plot_exposure_chain.R
R/plot_exposure_posteriors.R
R/plot_exposure_posteriors_bleed.R
R/plot_nnls_solution.R
R/plot_signature_pairwise_bleed.R
R/plot_two_signature_hexplot.R
R/reference_signatures_as_matrix.R
R/rotate_x_axis_labels.R
R/select_n_populations.R
R/stanmodels.R
R/subset_reference_signatures.R
R/trim_signature_names.R
README.md
SignIT.Rproj
configure
configure.win
data/example_catalog.RData
data/example_priors.Rdata
data/example_sv_catalog.RData
data/example_variants.RData
data/genome_exome_trinucleotide_frequencies.RData
data/missing_signature_demo_data.RData
data/nikzainal_sv_signatures.RData
data/wtsi_30_snv_signatures.RData
data/wtsi_30_snv_signatures_exome.RData
docs/SignIT_novel_signatures.html
docs/vignette.html
inst/include/stan_meta_header.hpp
inst/stan/include/license.stan
inst/stan/population_model.stan
inst/stan/signature_model.stan
inst/stan/signature_model_prior.stan
inst/stan/signit_model.stan
inst/stan/signit_model_infer_populations.stan
man/SignIT-package.Rd
man/all_snv_mutation_types.Rd
man/base_complement.Rd
man/collapse_mutation_types.Rd
man/collapse_signatures_by_bleed.Rd
man/collapse_signatures_by_bleed_all_solutions.Rd
man/compute_population_bic.Rd
man/compute_population_model_log_likelihood.Rd
man/compute_population_signatures_bic.Rd
man/compute_population_signatures_log_likelihood.Rd
man/compute_population_signatures_waic.Rd
man/compute_signatures_waic.Rd
man/get_density_mode.Rd
man/get_exposure_pairwise_correlations.Rd
man/get_exposure_summary_table.Rd
man/get_exposures.Rd
man/get_os.Rd
man/get_population_parameter_estimates.Rd
man/get_population_signatures.Rd
man/get_populations.Rd
man/get_reference_signatures.Rd
man/get_signature_bleed_graph.Rd
man/get_signature_names.Rd
man/get_snv_mutation_type.Rd
man/get_trinucleotide.Rd
man/get_vaf_correction.Rd
man/map_phi_to_population.Rd
man/map_phi_to_signature.Rd
man/map_population_signatures.Rd
man/mcmc_exposures_as_matrix.Rd
man/mutation_types_match.Rd
man/mutations_to_catalog.Rd
man/normalize_reference_signatures.Rd
man/parse_stan_output.Rd
man/plot_bleed_interactions.Rd
man/plot_exposure_chain.Rd
man/plot_exposure_posteriors.Rd
man/plot_exposure_posteriors_bleed.Rd
man/plot_nnls_solution.Rd
man/plot_population_signatures.Rd
man/plot_signature_pairwise_bleed.Rd
man/plot_two_signature_hexplot.Rd
man/reference_signatures_as_matrix.Rd
man/reverse_factor_levels.Rd
man/reverse_factor_ranks.Rd
man/rotate_x_axis_labels.Rd
man/select_n_populations.Rd
man/signature_present.Rd
man/stitch_mutation_types.Rd
man/subset_reference_signatures.Rd
man/summarise_population_signatures.Rd
man/trim_signature_names.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/RcppExports.o
src/SignIT.so
src/stanExports_population_model.cc
src/stanExports_population_model.h
src/stanExports_population_model.o
src/stanExports_signature_model.cc
src/stanExports_signature_model.h
src/stanExports_signature_model.o
src/stanExports_signature_model_prior.cc
src/stanExports_signature_model_prior.h
src/stanExports_signature_model_prior.o
src/stanExports_signit_model.cc
src/stanExports_signit_model.h
src/stanExports_signit_model.o
src/stanExports_signit_model_infer_populations.cc
src/stanExports_signit_model_infer_populations.h
src/stanExports_signit_model_infer_populations.o
vignette/Clonality_Modeling.Rmd
vignette/SignIT_novel_signatures.Rmd
vignette/SignIT_novel_signatures.html
vignette/SignIT_vignette.Rmd
vignette/SignIT_vignette.html
vignette/SignIT_vignette.md
