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

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/MutationalPatterns.R R/binomial_test.R R/cluster_signatures.R R/cos_sim.R R/cos_sim_matrix.R R/enrichment_depletion_test.R R/extract_signatures.R R/fit_to_signatures.R R/genomic_distribution.R R/intersect_with_region.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_compare_profiles.R R/plot_contribution.R R/plot_contribution_heatmap.R R/plot_cosine_heatmap.R R/plot_enrichment_depletion.R R/plot_rainfall.R R/plot_signature_strand_bias.R R/plot_spectrum.R R/plot_strand.R R/plot_strand_bias.R R/read_vcfs_as_granges.R R/strand_bias_test.R R/strand_occurrences.R R/type_context.R README.md
images/96_profile.png
images/contribution1.png
images/contribution2.png
images/contribution_cancer_sigs.png
images/estim_rank.png
images/genomic_distribution.png
images/original_VS_reconstructed.png
images/original_VS_reconstructed_cancer_sigs.png
images/rainfall1.png
images/rainfall2.png
images/signatures.png
images/signatures_strand.png
images/spectra1.png
images/spectra2.png
images/strand.png
inst/CITATION
inst/NEWS
inst/extdata/ReplicationDirectionRegions.bed
inst/extdata/callableloci-sample.bed
inst/extdata/colon1-sample.vcf
inst/extdata/colon2-sample.vcf
inst/extdata/colon3-sample.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_probabilities.txt
inst/states/CTCF_g_data.rds
inst/states/TF_binding_g_data.rds
inst/states/distr_data.rds
inst/states/genes_hg19.rds
inst/states/mut_mat_data.rds
inst/states/mut_mat_s_data.rds
inst/states/nmf_res_data.rds
inst/states/nmf_res_strand_data.rds
inst/states/open_g_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/regulatory_data.rds
man/MutationalPatterns-package.Rd man/binomial_test.Rd man/cluster_signatures.Rd man/cos_sim.Rd man/cos_sim_matrix.Rd man/enrichment_depletion_test.Rd man/explained_by_signatures.Rd man/extract_signatures.Rd man/fit_to_signatures.Rd man/genomic_distribution.Rd man/mut_context.Rd man/mut_matrix.Rd man/mut_matrix_stranded.Rd man/mut_strand.Rd man/mut_type.Rd man/mut_type_occurrences.Rd man/mutation_context.Rd man/mutation_types.Rd man/mutations_from_vcf.Rd man/plot_192_profile.Rd man/plot_96_profile.Rd man/plot_compare_profiles.Rd man/plot_contribution.Rd man/plot_contribution_heatmap.Rd man/plot_cosine_heatmap.Rd man/plot_enrichment_depletion.Rd man/plot_rainfall.Rd man/plot_signature_strand_bias.Rd man/plot_spectrum.Rd man/plot_strand.Rd man/plot_strand_bias.Rd man/read_vcfs_as_granges.Rd man/strand_bias_test.Rd man/strand_from_vcf.Rd man/strand_occurrences.Rd man/type_context.Rd paper/figures_paper.R tests/testthat.R tests/testthat/test_mut_matrix.R tests/testthat/test_mut_matrix_stranded.R tests/testthat/test_read_vcfs_as_granges.R
vignettes/Introduction_to_MutationalPatterns.Rnw
vignettes/references.bib
CuppenResearch/MutationalPatterns documentation built on May 4, 2018, 3:46 a.m.