| 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
|
| GenomeOfNl_raw |
Man page
|
| LCD |
Man page
Source code
|
| LCD_SMC |
Man page
Source code
|
| LCD_complex_cutoff |
Man page
Source code
|
| LCD_complex_cutoff_combined |
Man page
Source code
|
| LCD_complex_cutoff_consensus |
Man page
Source code
|
| LCD_complex_cutoff_perPID |
Man page
Source code
|
| LCD_cutoff |
Source code
|
| MutCat_indel_df |
Man page
|
| PCAWG_SP_ID_sigInd_df |
Man page
|
| PCAWG_SP_ID_sigs_df |
Man page
|
| PCAWG_SP_SBS_sigInd_Artif_df |
Man page
|
| PCAWG_SP_SBS_sigInd_Real_df |
Man page
|
| PCAWG_SP_SBS_sigs_Artif_df |
Man page
|
| PCAWG_SP_SBS_sigs_Real_df |
Man page
|
| SMC |
Man page
Source code
|
| SMC_perPID |
Man page
|
| YAPSA |
Man page
|
| add_annotation |
Man page
Source code
|
| add_as_fist_to_list |
Man page
Source code
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| add_rainfalls_track |
Source code
|
| add_rectangles_track |
Source code
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| adjust_number_of_columns_in_list_of_catalogues |
Source code
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| 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_exposures_list_barplot |
Man page
Source code
|
| annotation_heatmap_exposures |
Man page
Source code
|
| attribute_nucleotide_exchanges |
Man page
Source code
|
| attribute_sequence_contex_indel |
Man page
Source code
|
| attribution_of_indels |
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
|
| classify_indels |
Man page
Source code
|
| compare_SMCs |
Man page
Source code
|
| compare_exposures |
Man page
Source code
|
| compare_expousre_sets |
Man page
Source code
|
| compare_sets |
Man page
Source code
|
| compare_to_catalogues |
Man page
Source code
|
| complex_heatmap_exposures |
Man page
Source code
|
| computeLogLik |
Man page
Source code
|
| compute_comparison_stat_df |
Man page
Source code
|
| confIntExp |
Man page
Source code
|
| confidence_indel_calulation |
Man page
Source code
|
| confidence_indel_only_calulation |
Man page
Source code
|
| correct_rounded |
Man page
Source code
|
| cosineDist |
Man page
Source code
|
| cosineMatchDist |
Man page
Source code
|
| create_indel_mut_cat_from_df |
Man page
Source code
|
| create_indel_mutation_catalogue_from_df |
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
|
| cutoffPCAWG_ID_WGS_Pid_df |
Man page
|
| cutoffPCAWG_SBS_WGSWES_artifPid_df |
Man page
|
| cutoffPCAWG_SBS_WGSWES_realPid_df |
Man page
|
| cutoffs |
Man page
|
| cutoffs_pcawg |
Man page
|
| deriveSigInd_df |
Man page
Source code
|
| disambiguateVector |
Man page
Source code
|
| enhanced_barplot |
Source code
|
| enrichSigs |
Man page
Source code
|
| exampleINDEL_YAPSA |
Man page
|
| exampleYAPSA |
Man page
|
| exchange_colour_vector |
Man page
|
| exome_mutCatRaw_df |
Man page
|
| exposures_barplot |
Man page
Source code
|
| extract_names_from_gene_list |
Man page
Source code
|
| find_affected_PIDs |
Man page
Source code
|
| getSequenceContext |
Man page
Source code
|
| get_extreme_PIDs |
Man page
Source code
|
| hclust_exposures |
Man page
Source code
|
| logLikelihood |
Man page
Source code
|
| lymphomaNature2013_mutCat_df |
Man page
|
| 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
|
| plotExchangeSpectra_indel |
Man page
|
| plotExposuresConfidence |
Man page
Source code
|
| plotExposuresConfidence_indel |
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
|
| preprocess_VRanges |
Source code
|
| preprocess_data.frame |
Source code
|
| read_entry |
Man page
Source code
|
| read_list |
Man page
Source code
|
| rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df |
Man page
|
| relateSigs |
Man page
Source code
|
| repeat_df |
Man page
Source code
|
| res |
Source code
|
| round_precision |
Man page
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
|
| sigs_pcawg |
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
|
| temp_trellis_rainfall_plot |
Man page
Source code
|
| testSigs |
Man page
Source code
|
| 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
|
| trellis_rainfall_plot_old |
Man page
Source code
|
| uniquify |
Source code
|
| variateExp |
Man page
Source code
|
| variateExpSingle |
Man page
Source code
|
| vplayout |
Source code
|
