Files in YAPSA
Yet Another Package for Signature Analysis
LICENSE.txt
CONTRIBUTORS
README.md
NEWS
NAMESPACE
DESCRIPTION
README_files/figure-html/exposures_barplot_LCD_sig_ind-1.png
README_files/figure-html/make_rainfall_plot-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_cutoffZero-1.png
README_files/figure-html/exposures_barplot_rel_cutoffGen-1.png
README_files/figure-html/exposures_barplot_LCD-1.png
README_files/figure-html/exposures_barplot_abs_cutoffGen-1.png
README_files/figure-html/cluster_PIDs_sig_info-1.png
README_files/figure-html/apply_heatmap_exposures-1.png
README_files/figure-html/SMC_mut_density-1.png
README_files/figure-html/exposures_barplot_rel_cutoffSpec-1.png
build/vignette.rds
data/GenomeOfNl_MutCat.rda
data/lymphoma_Nature2013_raw.rda
data/cutoffs_pcawg.rda
data/GenomeOfNl_raw.rda
data/lymphoma_test.rda
data/sigs.rda
data/lymphoma_PID.rda
data/exchange_colour_vector.rda
data/lymphoma_cohort_LCD_results.rda
data/lymphomaNature2013_mutCat_df.rda
data/sigs_pcawg.rda
data/smallCellLungCancerMutCat_NatureGenetics2012.rda
data/cutoffs.rda
data/targetCapture_cor_factors.rda
R/plot_functions.R
R/indels.R
R/compare_SMCs.R
R/LCD.R
R/io_functions.R
R/complex_functions.R
R/confidence.R
R/interact_foreign.R
R/data.R
R/indel_functions.R
R/pkgname.R
R/global.R
R/SMC.R
R/basic_functions.R
vignettes/NMF.png
vignettes/YAPSA.Rmd
vignettes/vignette_confidenceIntervals.Rmd
vignettes/vignette_exomes.Rmd
vignettes/vignette_stratifiedAnalysis.Rmd
vignettes/vignette_signature_specific_cutoffs.Rmd
vignettes/vignettes_Indel.Rmd
man/hclust_exposures.Rd
man/GenomeOfNl_raw.Rd
man/stat_plot_subgroups.Rd
man/MutCat_indel_df.Rd
man/create_indel_mut_cat_from_df.Rd
man/LCD_SMC.Rd
man/extract_names_from_gene_list.Rd
man/stat_test_SMC.Rd
man/shapiro_if_possible.Rd
man/annotation_exposures_barplot.Rd
man/run_kmer_frequency_normalization.Rd
man/confidence_indel_only_calulation.Rd
man/lymphomaNature2013_mutCat_df.Rd
man/deriveSigInd_df.Rd
man/aggregate_exposures_by_category.Rd
man/confidence_indel_calulation.Rd
man/normalizeMotifs_otherRownames.Rd
man/make_catalogue_strata_df.Rd
man/computeLogLik.Rd
man/run_comparison_catalogues.Rd
man/LCD_complex_cutoff.Rd
man/run_kmer_frequency_correction.Rd
man/transform_rownames_R_to_MATLAB.Rd
man/attribute_sequence_contex_indel.Rd
man/trellis_rainfall_plot.Rd
man/SMC_perPID.Rd
man/get_extreme_PIDs.Rd
man/build_gene_list_for_pathway.Rd
man/add_annotation.Rd
man/SMC.Rd
man/stat_test_subgroups.Rd
man/run_comparison_general.Rd
man/split_exposures_by_subgroups.Rd
man/make_comparison_matrix.Rd
man/create_indel_mutation_catalogue_from_df.Rd
man/variateExpSingle.Rd
man/plot_SMC.Rd
man/cosineMatchDist.Rd
man/exampleINDEL_YAPSA.Rd
man/annotation_heatmap_exposures.Rd
man/exampleYAPSA.Rd
man/testSigs.Rd
man/read_entry.Rd
man/find_affected_PIDs.Rd
man/merge_exposures.Rd
man/variateExp.Rd
man/make_strata_df.Rd
man/melt_exposures.Rd
man/cut_breaks_as_intervals.Rd
man/plotExchangeSpectra_indel.Rd
man/run_SMC.Rd
man/add_as_fist_to_list.Rd
man/plot_strata.Rd
man/enrichSigs.Rd
man/annotation_exposures_list_barplot.Rd
man/sigs.Rd
man/disambiguateVector.Rd
man/plotExposuresConfidence_indel.Rd
man/make_subgroups_df.Rd
man/confIntExp.Rd
man/plot_exposures.Rd
man/cutoffs_pcawg.Rd
man/sum_over_list_of_df.Rd
man/targetCapture_cor_factors.Rd
man/YAPSA.Rd
man/translate_to_hg19.Rd
man/getSequenceContext.Rd
man/normalize_df_per_dim.Rd
man/logLikelihood.Rd
man/compare_expousre_sets.Rd
man/compare_to_catalogues.Rd
man/create_mutation_catalogue_from_VR.Rd
man/temp_trellis_rainfall_plot.Rd
man/repeat_df.Rd
man/annotate_intermut_dist_PID.Rd
man/test_gene_list_in_exposures.Rd
man/annotate_intermut_dist_cohort.Rd
man/compare_sets.Rd
man/create_mutation_catalogue_from_df.Rd
man/run_annotate_vcf_pl.Rd
man/relateSigs.Rd
man/correct_rounded.Rd
man/attribution_of_indels.Rd
man/complex_heatmap_exposures.Rd
man/LCD.Rd
man/cosineDist.Rd
man/attribute_nucleotide_exchanges.Rd
man/sigs_pcawg.Rd
man/plotExposuresConfidence.Rd
man/test_exposureAffected.Rd
man/compare_SMCs.Rd
man/stderrmean.Rd
man/round_precision.Rd
man/run_plot_strata_general.Rd
man/exchange_colour_vector.Rd
man/compare_exposures.Rd
man/compute_comparison_stat_df.Rd
man/trellis_rainfall_plot_old.Rd
man/classify_indels.Rd
man/cutoffs.Rd
man/exome_mutCatRaw_df.Rd
man/plotExchangeSpectra.Rd
man/makeVRangesFromDataFrame.Rd
man/exposures_barplot.Rd
tests/testthat.R
tests/testthat/test_complex_functions.R
tests/testthat/test_basic_functions.R
tests/testthat/test_LCD.R
inst/doc/vignette_signature_specific_cutoffs.R
inst/doc/index.html
inst/doc/vignette_exomes.html
inst/doc/vignette_confidenceIntervals.R
inst/doc/vignette_signature_specific_cutoffs.html
inst/doc/vignette_stratifiedAnalysis.html
inst/doc/YAPSA.Rmd
inst/doc/vignette_exomes.R
inst/doc/vignette_confidenceIntervals.Rmd
inst/doc/vignette_exomes.Rmd
inst/doc/YAPSA.R
inst/doc/vignettes_Indel.R
inst/doc/vignette_stratifiedAnalysis.R
inst/doc/YAPSA.html
inst/doc/vignette_stratifiedAnalysis.Rmd
inst/doc/vignette_confidenceIntervals.html
inst/doc/vignette_signature_specific_cutoffs.Rmd
inst/doc/vignettes_Indel.Rmd
inst/doc/vignettes_Indel.html
inst/foreign/annotate_vcf.pl
inst/foreign/kmer_frequencies.pl
inst/YAPSA_datasets/cutoffs_pcawg.rda
inst/YAPSA_datasets/sigs.rda
inst/YAPSA_datasets/sigs_pcawg.rda
inst/YAPSA_datasets/cutoffs.rda
