MutationalPatterns
Comprehensive genome-wide analysis of mutational processes

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Comprehensive genome-wide analysis of mutational processes

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README.md tests/testthat.R tests/testthat/test-plot_lesion_segregation.R tests/testthat/test-mut_matrix_stranded.R tests/testthat/test-get_indel_context.R tests/testthat/test-plot_rainfall.R tests/testthat/test-fit_to_signatures_bootstrapped.R tests/testthat/test-context_potential_damage_analysis.R tests/testthat/test-strand_bias_test.R tests/testthat/test-plot_contribution.R tests/testthat/test-mut_context.R tests/testthat/test-plot_main_dbs_contexts.R tests/testthat/test-plot_strand_bias.R tests/testthat/test-bin_mutation_density.R tests/testthat/test-get_known_signatures.R tests/testthat/test-count_mbs_contexts.R tests/testthat/test-get_dbs_context.R tests/testthat/test-count_indel_contexts.R tests/testthat/test-plot_original_vs_reconstructed.R tests/testthat/test-enrichment_depletion_test.R tests/testthat/test-rename_nmf_signatures.R tests/testthat/test-type_context.R tests/testthat/test-binomial_test.R tests/testthat/test-extract_signatures.R tests/testthat/test-cos_sim.R tests/testthat/test-plot_compare_dbs.R tests/testthat/test-calculate_lesion_segretation.R tests/testthat/test-fit_to_signatures.R tests/testthat/test-plot_spectrum_region.R tests/testthat/test-mut_type_occurrences.R tests/testthat/test-plot_spectrum.R tests/testthat/test-signature_potential_damage_analysis.R tests/testthat/test-plot_192_profile.R tests/testthat/test-plot_compare_mbs.R tests/testthat/test-plot_96_profile.R tests/testthat/test-plot_profile_heatmap.R tests/testthat/test-split_muts_region.R tests/testthat/test-genomic_distribution.R tests/testthat/test-plot_enrichment_depletion.R tests/testthat/test-plot_indel_contexts.R tests/testthat/test-get_mut_type.R tests/testthat/test-plot_dbs_contexts.R tests/testthat/test-plot_signature_strand_bias.R tests/testthat/test-strand_occurrences.R tests/testthat/test-plot_correlation_bootstrap.R tests/testthat/test-read_vcfs_as_granges.R tests/testthat/test-mut_type.R tests/testthat/test-merge_signatures.R tests/testthat/test-mut_matrix.R tests/testthat/test-plot_bootstrapped_contribution.R tests/testthat/test-plot_strand.R tests/testthat/test-cos_sim_matrix.R tests/testthat/test-plot_long_profile.R tests/testthat/test-pool_mut_matrix.R tests/testthat/test-plot_compare_indels.R tests/testthat/test-plot_main_indel_contexts.R tests/testthat/test-plot_compare_profiles.R tests/testthat/test-plot_cosine_heatmap.R tests/testthat/test-count_dbs_contexts.R tests/testthat/test-plot_river.R tests/testthat/test-fit_to_signatures_strict.R tests/testthat/test-lengthen_mut_matrix.R tests/testthat/test-plot_mbs_contexts.R tests/testthat/test-convert_sigs_to_ref.R tests/testthat/test-plot_contribution_heatmap.R tests/testthat/test-mutations_from_vcf.R R/count_mbs_contexts.R R/count_indel_contexts.R R/get_dbs_context.R R/plot_contribution_heatmap.R R/type_context.R R/signature_potential_damage_analysis.R R/fit_to_signatures.R R/plot_dbs_contexts.R R/mut_192_occurrences.R R/MutationalPatterns.R R/plot_strand.R R/intersect_with_region.R R/pool_mut_matrix.R R/plot_profile_region.R R/read_vcfs_as_granges.R R/plot_enrichment_depletion.R R/get_ref_alt.R R/plot_profile_heatmap.R R/plot_strand_bias.R R/plot_spectrum_region.R R/mut_strand.R R/plot_spectrum.R R/cluster_signatures.R R/extract_signatures.R R/mut_type.R R/plot_192_profile.R R/calculate_lesion_segretation.R R/genomic_distribution.R R/mutations_from_vcf.R R/bin_mutation_density.R R/plot_river.R R/plot_indel_contexts.R R/fit_to_signatures_strict.R R/cos_sim.R R/strand_bias_test.R R/plot_cosine_heatmap.R R/enrichment_depletion_test.R R/mut_matrix_stranded.R R/plot_original_vs_reconstructed.R R/fit_to_signatures_bootstrapped.R R/get_sig_start.R R/strand_occurrences.R R/mut_context.R R/plot_mbs_contexts.R R/plot_contribution.R R/plot_compare_dbs.R R/plot_compare_profiles.R R/plot_compare_mbs.R R/plot_main_dbs_contexts.R R/split_muts_region.R R/get_mut_type.R R/mut_type_occurrences.R R/get_indel_context.R R/binomial_test.R R/plot_96_profile.R R/count_dbs_contexts.R R/context_potential_damage_analysis.R R/plot_bootstrapped_contribution.R R/check_remove_muttypes.R R/rename_nmf_signatures.R R/plot_rainfall.R R/lengthen_mut_matrix.R R/plot_compare_indels.R R/mut_96_occurrences.R R/convert_sigs_to_ref.R R/plot_lesion_segregation.R R/merge_signatures.R R/plot_main_indel_contexts.R R/get_known_signatures.R R/cos_sim_matrix.R R/plot_correlation_bootstrap.R R/mut_matrix.R R/plot_signature_strand_bias.R man/plot_river.Rd man/plot_compare_profiles.Rd man/mut_context.Rd man/plot_compare_mbs.Rd man/get_known_signatures.Rd man/plot_spectrum.Rd man/plot_lesion_segregation.Rd man/fit_to_signatures.Rd man/mut_matrix_stranded.Rd man/count_mbs_contexts.Rd man/merge_signatures.Rd man/genomic_distribution.Rd man/plot_192_profile.Rd man/plot_spectrum_region.Rd man/extract_signatures.Rd man/plot_signature_strand_bias.Rd man/plot_96_profile.Rd man/plot_original_vs_reconstructed.Rd man/mut_type_occurrences.Rd man/MutationalPatterns-defunct.Rd man/read_vcfs_as_granges.Rd man/plot_mbs_contexts.Rd man/plot_dbs_contexts.Rd man/plot_cosine_heatmap.Rd man/fit_to_signatures_bootstrapped.Rd man/signature_potential_damage_analysis.Rd man/plot_profile_region.Rd man/count_indel_contexts.Rd man/get_mut_type.Rd man/mut_matrix.Rd man/enrichment_depletion_test.Rd man/plot_indel_contexts.Rd man/binomial_test.Rd man/get_dbs_context.Rd man/mut_192_occurrences.Rd man/plot_strand_bias.Rd man/mutations_from_vcf.Rd man/count_dbs_contexts.Rd man/plot_strand.Rd man/MutationalPatterns-package.Rd man/mut_type.Rd man/plot_main_indel_contexts.Rd man/get_indel_context.Rd man/cluster_signatures.Rd man/context_potential_damage_analysis.Rd man/mut_strand.Rd man/mut_96_occurrences.Rd man/strand_bias_test.Rd man/plot_enrichment_depletion.Rd man/plot_bootstrapped_contribution.Rd man/type_context.Rd man/plot_profile_heatmap.Rd man/bin_mutation_density.Rd man/plot_contribution.Rd man/plot_compare_indels.Rd man/rename_nmf_signatures.Rd man/strand_occurrences.Rd man/plot_rainfall.Rd man/plot_main_dbs_contexts.Rd man/split_muts_region.Rd man/plot_contribution_heatmap.Rd man/plot_correlation_bootstrap.Rd man/pool_mut_mat.Rd man/calculate_lesion_segregation.Rd man/cos_sim.Rd man/plot_compare_dbs.Rd man/fit_to_signatures_strict.Rd man/convert_sigs_to_ref.Rd man/cos_sim_matrix.Rd man/lengthen_mut_matrix.Rd
inst/CITATION
inst/NEWS
inst/extdata/colon2-sample.vcf
inst/extdata/colon3-sample.vcf
inst/extdata/blood-BCH.vcf
inst/extdata/liver1-sample.vcf
inst/extdata/blood-ACC55.vcf
inst/extdata/ReplicationDirectionRegions.bed
inst/extdata/empty.vcf
inst/extdata/colon1-sample.vcf
inst/extdata/callableloci-sample.bed
inst/extdata/blood-AC.vcf
inst/extdata/liver3-sample.vcf
inst/extdata/intestine2-sample.vcf
inst/extdata/intestine1-sample.vcf
inst/extdata/liver2-sample.vcf
inst/extdata/intestine3-sample.vcf
inst/extdata/signatures/dbs_SIGNAL_exposure.txt
inst/extdata/signatures/SIGNAL_conversion_matrix.txt
inst/extdata/signatures/snv_SPARSE_reference.txt
inst/extdata/signatures/snv_SIGNAL_tissue.txt
inst/extdata/signatures/tsb_snv_COSMIC_reference.txt
inst/extdata/signatures/snv_COSMIC_reference.txt
inst/extdata/signatures/indel_COSMIC_reference.txt
inst/extdata/signatures/dbs_COSMIC_reference.txt
inst/extdata/signatures/snv_SIGNAL_exposure.txt
inst/extdata/signatures/snv_SIGNAL_reference.txt
inst/doc/Introduction_to_MutationalPatterns.Rmd
inst/doc/Introduction_to_MutationalPatterns.html
inst/doc/Introduction_to_MutationalPatterns.R inst/scripts/create_example_indels.R inst/scripts/create_example_regulatory_regions.R inst/scripts/create_example_snvs.R inst/scripts/create_example_vcfs.R inst/scripts/create_example_dbs.R inst/scripts/Format_signatures.R inst/scripts/create_example_mbs.R
inst/states/blood_grl_indel_context.rds
inst/states/distr_data.rds
inst/states/blosum62.rds
inst/states/mut_mat_s_data.rds
inst/states/snv_refit.rds
inst/states/mut_mat_longregions.rds
inst/states/blood_indels_counts_split_region.rds
inst/states/nmf_res_strand_data.rds
inst/states/grl_split_region.rds
inst/states/blood_grl.rds
inst/states/dbs_refit.rds
inst/states/promoter_g_data.rds
inst/states/blood_mbs_counts.rds
inst/states/blood_indels_longmatrix_split_region.rds
inst/states/blood_indel_counts.rds
inst/states/CTCF_g_data.rds
inst/states/blood_grl_dbs_context.rds
inst/states/blood_dbs_counts.rds
inst/states/indel_refit.rds
inst/states/read_vcfs_as_granges_output.rds
inst/states/lesion_segregation.rds
inst/states/blood_grl_indel.rds
inst/states/regulatory_data.rds
inst/states/strict_snv_refit.rds
inst/states/blood_grl_dbs.rds
inst/states/nmf_res_data.rds
inst/states/repli_strand.rds
inst/states/mut_mat_data_extended.rds
inst/states/promoter_flanking_g_data.rds
inst/states/mut_mat_repli.rds
inst/states/blood_grl_mbs.rds
inst/states/context_mismatches.rds
inst/states/mut_mat_splitregions.rds
inst/states/bootstrapped_snv_refit.rds
inst/states/mut_mat_data.rds
build/vignette.rds
vignettes/Introduction_to_MutationalPatterns.Rmd
vignettes/references.bib
MutationalPatterns documentation built on Nov. 14, 2020, 2:03 a.m.

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