MutationalPatterns: Studying patterns in base substitution catalogues

An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.

AuthorFrancis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen
Date of publicationNone
MaintainerFrancis Blokzijl <F.Blokzijl@umcutrecht.nl>, Roel Janssen <R.R.E.Janssen-10@umcutrecht.nl>
LicenseMIT + file LICENSE
Version1.0.0
https://github.com/CuppenResearch/MutationalPatterns

View on Bioconductor

Man pages

binomial_test: Binomial test for enrichment or depletion testing

enrichment_depletion_test: Test for enrichment or depletion of mutations in genomic...

extract_signatures: Extract mutational signatures from 96 mutation matrix using...

fit_to_signatures: Find optimal nonnegative linear combination of mutation...

genomic_distribution: Find overlaps between mutations and a genomic region.

intersect_with_region: Find overlap between mutations and a genomic region

mut_192_occurrences: Count 96 trinucleotide mutation occurrences with...

mut_96_occurrences: Count 96 trinucleotide mutation occurrences

MutationalPatterns-package: MutationalPatterns: an integrative R package for studying...

mutation_context: Retrieve context of base substitutions

mutations_from_vcf: Retrieve base substitutions from vcf

mutation_types: Retrieve base substitution types from a VCF object

mut_matrix: Make mutation count matrix of 96 trinucleotides

mut_matrix_stranded: Make mutation count matrix of 96 trinucleotides with...

mut_type_occurrences: Count the occurrences of each base substitution type

plot_192_profile: Plot 192 trinucleotide profile

plot_96_profile: Plot 96 trinucleotide profile

plot_compare_profiles: Compare two 96 mutation profiles

plot_contribution: Plot signature contribution

plot_enrichment_depletion: Plot enrichment/depletion of mutations in genomic regions

plot_rainfall: Plot genomic rainfall

plot_signature_strand_bias: Plot signature strand bias

plot_spectrum: Plot point mutation spectrum

plot_strand: Plot strand per base substitution type

plot_strand_bias: Plot strand bias per base substitution type

read_vcfs_as_granges: Read VCF files into a GRangesList

strand_bias_test: Significance test for transcriptional strand asymmetry

strand_from_vcf: Find transcriptional strand of base substitutions in vcf

strand_occurrences: Count occurrences per base substitution type and...

type_context: Retrieve context of base substitution types

Files in this package

MutationalPatterns/DESCRIPTION
MutationalPatterns/LICENSE
MutationalPatterns/NAMESPACE
MutationalPatterns/R
MutationalPatterns/R/Defunct.R MutationalPatterns/R/MutationalPatterns.R MutationalPatterns/R/binomial_test.R MutationalPatterns/R/enrichment_depletion_test.R MutationalPatterns/R/extract_signatures.R MutationalPatterns/R/fit_to_signatures.R MutationalPatterns/R/genomic_distribution.R MutationalPatterns/R/intersect_with_region.R MutationalPatterns/R/mut_192_occurrences.R MutationalPatterns/R/mut_96_occurrences.R MutationalPatterns/R/mut_matrix.R MutationalPatterns/R/mut_matrix_stranded.R MutationalPatterns/R/mut_type_occurrences.R MutationalPatterns/R/mutation_context.R MutationalPatterns/R/mutation_types.R MutationalPatterns/R/mutations_from_vcf.R MutationalPatterns/R/plot_192_profile.R MutationalPatterns/R/plot_96_profile.R MutationalPatterns/R/plot_compare_profiles.R MutationalPatterns/R/plot_contribution.R MutationalPatterns/R/plot_enrichment_depletion.R MutationalPatterns/R/plot_rainfall.R MutationalPatterns/R/plot_signature_strand_bias.R MutationalPatterns/R/plot_spectrum.R MutationalPatterns/R/plot_strand.R MutationalPatterns/R/plot_strand_bias.R MutationalPatterns/R/read_vcfs_as_granges.R MutationalPatterns/R/strand_bias_test.R MutationalPatterns/R/strand_from_vcf.R MutationalPatterns/R/strand_occurrences.R MutationalPatterns/R/type_context.R
MutationalPatterns/README.md
MutationalPatterns/build
MutationalPatterns/build/vignette.rds
MutationalPatterns/images
MutationalPatterns/images/96_profile.png
MutationalPatterns/images/contribution1.png
MutationalPatterns/images/contribution2.png
MutationalPatterns/images/contribution_cancer_sigs.png
MutationalPatterns/images/estim_rank.png
MutationalPatterns/images/genomic_distribution.png
MutationalPatterns/images/original_VS_reconstructed.png
MutationalPatterns/images/original_VS_reconstructed_cancer_sigs.png
MutationalPatterns/images/rainfall1.png
MutationalPatterns/images/rainfall2.png
MutationalPatterns/images/signatures.png
MutationalPatterns/images/signatures_strand.png
MutationalPatterns/images/spectra1.png
MutationalPatterns/images/spectra2.png
MutationalPatterns/images/strand.png
MutationalPatterns/inst
MutationalPatterns/inst/NEWS
MutationalPatterns/inst/doc
MutationalPatterns/inst/doc/MutationalPatterns.R
MutationalPatterns/inst/doc/MutationalPatterns.Rnw
MutationalPatterns/inst/doc/MutationalPatterns.pdf
MutationalPatterns/inst/extdata
MutationalPatterns/inst/extdata/callableloci-sample.bed
MutationalPatterns/inst/extdata/colon1-sample.vcf
MutationalPatterns/inst/extdata/colon2-sample.vcf
MutationalPatterns/inst/extdata/colon3-sample.vcf
MutationalPatterns/inst/extdata/intestine1-sample.vcf
MutationalPatterns/inst/extdata/intestine2-sample.vcf
MutationalPatterns/inst/extdata/intestine3-sample.vcf
MutationalPatterns/inst/extdata/liver1-sample.vcf
MutationalPatterns/inst/extdata/liver2-sample.vcf
MutationalPatterns/inst/extdata/liver3-sample.vcf
MutationalPatterns/inst/extdata/signatures_probabilities.txt
MutationalPatterns/inst/states
MutationalPatterns/inst/states/CTCF_g_data.rds
MutationalPatterns/inst/states/TF_binding_g_data.rds
MutationalPatterns/inst/states/distr_data.rds
MutationalPatterns/inst/states/genes_hg19.rds
MutationalPatterns/inst/states/mut_mat_data.rds
MutationalPatterns/inst/states/mut_mat_s_data.rds
MutationalPatterns/inst/states/nmf_res_data.rds
MutationalPatterns/inst/states/nmf_res_strand_data.rds
MutationalPatterns/inst/states/open_g_data.rds
MutationalPatterns/inst/states/promoter_flanking_g_data.rds
MutationalPatterns/inst/states/promoter_g_data.rds
MutationalPatterns/inst/states/read_vcfs_as_granges_output.rds
MutationalPatterns/inst/states/regulatory_data.rds
MutationalPatterns/man
MutationalPatterns/man/MutationalPatterns-package.Rd MutationalPatterns/man/binomial_test.Rd MutationalPatterns/man/enrichment_depletion_test.Rd MutationalPatterns/man/extract_signatures.Rd MutationalPatterns/man/fit_to_signatures.Rd MutationalPatterns/man/genomic_distribution.Rd MutationalPatterns/man/intersect_with_region.Rd MutationalPatterns/man/mut_192_occurrences.Rd MutationalPatterns/man/mut_96_occurrences.Rd MutationalPatterns/man/mut_matrix.Rd MutationalPatterns/man/mut_matrix_stranded.Rd MutationalPatterns/man/mut_type_occurrences.Rd MutationalPatterns/man/mutation_context.Rd MutationalPatterns/man/mutation_types.Rd MutationalPatterns/man/mutations_from_vcf.Rd MutationalPatterns/man/plot_192_profile.Rd MutationalPatterns/man/plot_96_profile.Rd MutationalPatterns/man/plot_compare_profiles.Rd MutationalPatterns/man/plot_contribution.Rd MutationalPatterns/man/plot_enrichment_depletion.Rd MutationalPatterns/man/plot_rainfall.Rd MutationalPatterns/man/plot_signature_strand_bias.Rd MutationalPatterns/man/plot_spectrum.Rd MutationalPatterns/man/plot_strand.Rd MutationalPatterns/man/plot_strand_bias.Rd MutationalPatterns/man/read_vcfs_as_granges.Rd MutationalPatterns/man/strand_bias_test.Rd MutationalPatterns/man/strand_from_vcf.Rd MutationalPatterns/man/strand_occurrences.Rd MutationalPatterns/man/type_context.Rd
MutationalPatterns/vignettes
MutationalPatterns/vignettes/MutationalPatterns.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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