API for huebschm/YAPSA
Yet Another Package for Signature Analysis
| Global functions | |
|---|---|
| AlexCosmicArtif_sigInd_df | Man page |
| AlexCosmicArtif_sig_df | Man page |
| AlexCosmicValid_sigInd_df | Man page |
| AlexCosmicValid_sig_df | Man page |
| AlexInitialArtif_sigInd_df | Man page |
| AlexInitialArtif_sig_df | Man page |
| AlexInitialValid_sigInd_df | Man page |
| AlexInitialValid_sig_df | Man page |
| COSMIC_subgroups_df | Man page |
| LCD | Man page Source code |
| LCD_SMC | Source code |
| LCD_complex_cutoff | Man page Source code |
| LCD_complex_cutoff_perPID | Man page Source code |
| LCD_cutoff | Source code |
| SMC | Source code |
| YAPSA | Man page |
| YAPSA-package | Man page |
| add_annotation | Man page Source code |
| add_as_fist_to_list | Man page Source code |
| adjust_number_of_columns_in_list_of_catalogues | Source code |
| aggregate_exposures_by_category | Man page Source code |
| annotate_intermut_dist_PID | Man page Source code |
| annotate_intermut_dist_cohort | Man page Source code |
| annotation_exposures_barplot | Man page Source code |
| annotation_heatmap_exposures | Man page Source code |
| attribute_nucleotide_exchanges | Man page Source code |
| average_over_present | Man page Source code |
| build_gene_list_for_pathway | Man page Source code |
| check_bedtools | Source code |
| check_perl | Source code |
| chosen_AlexInitialArtif_sigInd_df | Man page |
| chosen_signatures_indices_df | Man page |
| compare_SMCs | Man page Source code |
| compare_exposures | Man page Source code |
| compare_sets | Man page Source code |
| compare_to_catalogues | Man page Source code |
| complex_heatmap_exposures | Man page Source code |
| compute_comparison_stat_df | Man page Source code |
| cosineDist | Man page Source code |
| create_mutation_catalogue_from_VR | Man page Source code |
| create_mutation_catalogue_from_df | Man page Source code |
| cut_breaks_as_intervals | Man page Source code |
| cutoffCosmicArtif_abs_df | Man page |
| cutoffCosmicArtif_rel_df | Man page |
| cutoffCosmicValid_abs_df | Man page |
| cutoffCosmicValid_rel_df | Man page |
| cutoffInitialArtif_abs_df | Man page |
| cutoffInitialArtif_rel_df | Man page |
| cutoffInitialValid_abs_df | Man page |
| cutoffInitialValid_rel_df | Man page |
| cutoffs | Man page |
| enhanced_barplot | Source code |
| exampleYAPSA | Man page |
| exchange_colour_vector | Man page |
| exposures_barplot | Man page Source code |
| extract_names_from_gene_list | Man page Source code |
| find_affected_PIDs | Man page Source code |
| get_extreme_PIDs | Man page Source code |
| hclust_exposures | Man page Source code |
| lymphoma_Nature2013_COSMIC_cutoff_exposures_df | Man page |
| lymphoma_Nature2013_raw_df | Man page |
| lymphoma_PID_df | Man page |
| lymphoma_test_df | Man page |
| makeVRangesFromDataFrame | Man page Source code |
| make_catalogue_strata_df | Man page Source code |
| make_comparison_matrix | Man page Source code |
| make_strata_df | Man page Source code |
| make_subgroups_df | Man page Source code |
| melt_exposures | Man page Source code |
| merge_exposures | Man page Source code |
| norm_res | Source code |
| normalizeMotifs_otherRownames | Man page Source code |
| normalize_df_per_dim | Man page Source code |
| plotExchangeSpectra | Man page Source code |
| plot_SMC | Man page Source code |
| plot_SMC_PID_facet | Source code |
| plot_SMC_old | Source code |
| plot_colour_legend_subgroups | Source code |
| plot_exposures | Man page Source code |
| plot_exposures_old | Source code |
| plot_group_facet | Source code |
| plot_relative_exposures | Man page Source code |
| plot_strata | Man page Source code |
| rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df | Man page |
| repeat_df | Man page Source code |
| res | Source code |
| run_SMC | Man page Source code |
| run_annotate_vcf_pl | Man page Source code |
| run_bedtools_getfasta | Source code |
| run_comparison_catalogues | Man page Source code |
| run_comparison_general | Man page Source code |
| run_kmer_frequency_correction | Man page Source code |
| run_kmer_frequency_normalization | Man page Source code |
| run_kmer_frequency_pl | Source code |
| run_plot_strata_general | Man page Source code |
| save_mutation_catalogue | Source code |
| save_stratified_vcf_like_df | Source code |
| sd_over_present | Man page Source code |
| shapiro_if_possible | Man page Source code |
| sigs | Man page |
| split_exposures_by_subgroups | Man page Source code |
| stat_plot_subgroups | Man page Source code |
| stat_plot_subgroups_old | Source code |
| stat_test_SMC | Man page Source code |
| stat_test_subgroups | Man page Source code |
| stderrmean | Man page Source code |
| stderrmean_over_present | Man page Source code |
| stratify_and_create_mutational_catalogue | Source code |
| stratify_vcf_like_df | Source code |
| sum_over_list_of_df | Man page Source code |
| targetCapture_cor_factors | Man page |
| test_exposureAffected | Man page Source code |
| test_gene_list_in_exposures | Man page Source code |
| transform_rownames_MATLAB_to_R | Man page Source code |
| transform_rownames_R_to_MATLAB | Man page Source code |
| transform_rownames_YAPSA_to_deconstructSigs | Man page Source code |
| transform_rownames_deconstructSigs_to_YAPSA | Man page Source code |
| transform_rownames_nature_to_R | Man page Source code |
| translate_to_1kG | Man page Source code |
| translate_to_hg19 | Man page Source code |
| trellis_rainfall_plot | Man page Source code |
| vplayout | Source code |
