Files in eilslabs/YAPSA
Yet Another Package for Signature Analysis
CONTRIBUTORS
DESCRIPTION
LICENSE.txt
NAMESPACE
NEWS
R/LCD.R
R/SMC.R
R/basic_functions.R
R/compare_SMCs.R
R/complex_functions.R
R/data.R
R/interact_foreign.R
R/pkgname.R
R/plot_functions.R
README.md
README_files/figure-html/SMC_mut_density-1.png
README_files/figure-html/apply_heatmap_exposures-1.png
README_files/figure-html/cluster_PIDs_sig_info-1.png
README_files/figure-html/exposures_barplot_LCD-1.png
README_files/figure-html/exposures_barplot_LCD_sig_ind-1.png
README_files/figure-html/exposures_barplot_abs_cutoffGen-1.png
README_files/figure-html/exposures_barplot_abs_cutoffSpec-1.png
README_files/figure-html/exposures_barplot_abs_cutoffZero-1.png
README_files/figure-html/exposures_barplot_rel_cutoffGen-1.png
README_files/figure-html/exposures_barplot_rel_cutoffSpec-1.png
README_files/figure-html/exposures_barplot_rel_cutoffZero-1.png
README_files/figure-html/make_rainfall_plot-1.png
data/cutoffs.rda
data/exchange_colour_vector.rda
data/lymphoma_Nature2013_raw.rda
data/lymphoma_PID.rda
data/lymphoma_cohort_LCD_results.rda
data/lymphoma_test.rda
data/sigs.rda
data/targetCapture_cor_factors.rda
inst/foreign/annotate_vcf.pl
inst/foreign/kmer_frequencies.pl
man/LCD.Rd
man/LCD_complex_cutoff.Rd
man/YAPSA.Rd
man/add_annotation.Rd
man/add_as_fist_to_list.Rd
man/aggregate_exposures_by_category.Rd
man/annotate_intermut_dist_PID.Rd
man/annotate_intermut_dist_cohort.Rd
man/annotation_exposures_barplot.Rd
man/annotation_heatmap_exposures.Rd
man/attribute_nucleotide_exchanges.Rd
man/build_gene_list_for_pathway.Rd
man/compare_SMCs.Rd
man/compare_exposures.Rd
man/compare_sets.Rd
man/compare_to_catalogues.Rd
man/complex_heatmap_exposures.Rd
man/compute_comparison_stat_df.Rd
man/cosineDist.Rd
man/create_mutation_catalogue_from_VR.Rd
man/create_mutation_catalogue_from_df.Rd
man/cut_breaks_as_intervals.Rd
man/cutoffs.Rd
man/exampleYAPSA.Rd
man/exchange_colour_vector.Rd
man/exposures_barplot.Rd
man/extract_names_from_gene_list.Rd
man/find_affected_PIDs.Rd
man/get_extreme_PIDs.Rd
man/hclust_exposures.Rd
man/makeVRangesFromDataFrame.Rd
man/make_catalogue_strata_df.Rd
man/make_comparison_matrix.Rd
man/make_strata_df.Rd
man/make_subgroups_df.Rd
man/melt_exposures.Rd
man/merge_exposures.Rd
man/normalizeMotifs_otherRownames.Rd
man/normalize_df_per_dim.Rd
man/plotExchangeSpectra.Rd
man/plot_SMC.Rd
man/plot_exposures.Rd
man/plot_strata.Rd
man/repeat_df.Rd
man/run_SMC.Rd
man/run_annotate_vcf_pl.Rd
man/run_comparison_catalogues.Rd
man/run_comparison_general.Rd
man/run_kmer_frequency_correction.Rd
man/run_kmer_frequency_normalization.Rd
man/run_plot_strata_general.Rd
man/shapiro_if_possible.Rd
man/sigs.Rd
man/split_exposures_by_subgroups.Rd
man/stat_plot_subgroups.Rd
man/stat_test_SMC.Rd
man/stat_test_subgroups.Rd
man/stderrmean.Rd
man/sum_over_list_of_df.Rd
man/targetCapture_cor_factors.Rd
man/test_exposureAffected.Rd
man/test_gene_list_in_exposures.Rd
man/transform_rownames_R_to_MATLAB.Rd
man/translate_to_hg19.Rd
man/trellis_rainfall_plot.Rd
tests/testthat.R
tests/testthat/test_LCD.R
tests/testthat/test_basic_functions.R
tests/testthat/test_complex_functions.R
vignettes/.directory
vignettes/NMF.png
vignettes/YAPSA.Rmd
