Files in UMCUGenetics/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/MutationalPatterns.R R/S4_class.R R/bin_mutation_density.R R/binomial_test.R R/calculate_lesion_segretation.R R/check_remove_muttypes.R R/cluster_signatures.R R/context_potential_damage_analysis.R R/convert_sigs_to_ref.R R/cos_sim.R R/cos_sim_matrix.R R/count_dbs_contexts.R R/count_indel_contexts.R R/count_mbs_contexts.R R/determine_regional_similarity.R R/enrichment_depletion_test.R R/extract_signatures.R R/fit_to_signatures.R R/fit_to_signatures_bootstrapped.R R/fit_to_signatures_strict.R R/genomic_distribution.R R/get_dbs_context.R R/get_indel_context.R R/get_known_signatures.R R/get_mut_type.R R/get_ref_alt.R R/get_sig_start.R R/intersect_with_region.R R/lengthen_mut_matrix.R R/merge_signatures.R R/mut_192_occurrences.R R/mut_96_occurrences.R R/mut_context.R R/mut_matrix.R R/mut_matrix_stranded.R R/mut_strand.R R/mut_type.R R/mut_type_occurrences.R R/mutations_from_vcf.R R/plot_192_profile.R R/plot_96_profile.R R/plot_bootstrapped_contribution.R R/plot_compare_dbs.R R/plot_compare_indels.R R/plot_compare_mbs.R R/plot_compare_profiles.R R/plot_contribution.R R/plot_contribution_heatmap.R R/plot_correlation_bootstrap.R R/plot_cosine_heatmap.R R/plot_dbs_contexts.R R/plot_enrichment_depletion.R R/plot_indel_contexts.R R/plot_lesion_segregation.R R/plot_main_dbs_contexts.R R/plot_main_indel_contexts.R R/plot_mbs_contexts.R R/plot_original_vs_reconstructed.R R/plot_profile_heatmap.R R/plot_profile_region.R R/plot_rainfall.R R/plot_regional_similarity.R R/plot_river.R R/plot_signature_strand_bias.R R/plot_spectrum.R R/plot_spectrum_region.R R/plot_strand.R R/plot_strand_bias.R R/pool_mut_matrix.R R/read_vcfs_as_granges.R R/rename_nmf_signatures.R R/signature_potential_damage_analysis.R R/split_muts_region.R R/strand_bias_test.R R/strand_occurrences.R R/strict_refit_backwards_selection_sample.R R/strict_refit_best_subset_selection_sample.R R/type_context.R README.md

inst/CITATION

inst/NEWS

inst/extdata/ReplicationDirectionRegions.bed

inst/extdata/blood-AC.vcf

inst/extdata/blood-ACC55.vcf

inst/extdata/blood-BCH.vcf

inst/extdata/callableloci-sample.bed

inst/extdata/colon1-sample.vcf

inst/extdata/colon2-sample.vcf

inst/extdata/colon3-sample.vcf

inst/extdata/duplicate.vcf

inst/extdata/empty.vcf

inst/extdata/intestine1-sample.vcf

inst/extdata/intestine2-sample.vcf

inst/extdata/intestine3-sample.vcf

inst/extdata/liver1-sample.vcf

inst/extdata/liver2-sample.vcf

inst/extdata/liver3-sample.vcf

inst/extdata/signatures/SIGNAL_conversion_matrix.txt

inst/extdata/signatures/dbs_COSMIC_v3.1_reference.txt

inst/extdata/signatures/dbs_COSMIC_v3.2_reference_GRCh37.txt

inst/extdata/signatures/dbs_COSMIC_v3.2_reference_GRCh38.txt

inst/extdata/signatures/dbs_COSMIC_v3.2_reference_mm10.txt

inst/extdata/signatures/dbs_SIGNAL_exposure.txt

inst/extdata/signatures/indel_COSMIC_v3.1_reference.txt

inst/extdata/signatures/indel_COSMIC_v3.2_reference_GRCh37.txt

inst/extdata/signatures/snv_COSMIC_v3.1_reference.txt

inst/extdata/signatures/snv_COSMIC_v3.2_reference_GRCh37.txt

inst/extdata/signatures/snv_COSMIC_v3.2_reference_GRCh38.txt

inst/extdata/signatures/snv_COSMIC_v3.2_reference_mm10.txt

inst/extdata/signatures/snv_SIGNAL_exposure.txt

inst/extdata/signatures/snv_SIGNAL_reference.txt

inst/extdata/signatures/snv_SIGNAL_tissue.txt

inst/extdata/signatures/snv_SPARSE_reference.txt

inst/extdata/signatures/tsb_snv_COSMIC_v3.1_reference.txt

inst/scripts/Format_signatures.R inst/scripts/create_example_dbs.R inst/scripts/create_example_indels.R inst/scripts/create_example_mbs.R inst/scripts/create_example_regulatory_regions.R inst/scripts/create_example_snvs.R inst/scripts/create_example_vcfs.R

inst/states/CTCF_g_data.rds

inst/states/blood_dbs_counts.rds

inst/states/blood_grl.rds

inst/states/blood_grl_dbs.rds

inst/states/blood_grl_dbs_context.rds

inst/states/blood_grl_indel.rds

inst/states/blood_grl_indel_context.rds

inst/states/blood_grl_mbs.rds

inst/states/blood_indel_counts.rds

inst/states/blood_indels_counts_split_region.rds

inst/states/blood_indels_longmatrix_split_region.rds

inst/states/blood_mbs_counts.rds

inst/states/blosum62.rds

inst/states/bootstrapped_snv_refit.rds

inst/states/context_mismatches.rds

inst/states/dbs_refit.rds

inst/states/distr_data.rds

inst/states/grl_split_region.rds

inst/states/indel_refit.rds

inst/states/lesion_segregation.rds

inst/states/mut_mat_data.rds

inst/states/mut_mat_data_extended.rds

inst/states/mut_mat_longregions.rds

inst/states/mut_mat_repli.rds

inst/states/mut_mat_s_data.rds

inst/states/mut_mat_splitregions.rds

inst/states/nmf_res_data.rds

inst/states/nmf_res_strand_data.rds

inst/states/promoter_flanking_g_data.rds

inst/states/promoter_g_data.rds

inst/states/read_vcfs_as_granges_output.rds

inst/states/regional_sims.rds

inst/states/regulatory_data.rds

inst/states/repli_strand.rds

inst/states/snv_refit.rds

inst/states/strict_best_snv_refit.rds

inst/states/strict_snv_refit.rds

vignettes/references.bib

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.

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UMCUGenetics/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes

Files in UMCUGenetics/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes

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UMCUGenetics/MutationalPatterns Comprehensive genome-wide analysis of mutational processes

Files in UMCUGenetics/MutationalPatterns Comprehensive genome-wide analysis of mutational processes

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We want your feedback!

UMCUGenetics/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes

Files in UMCUGenetics/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes