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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MutationalPatterns")
AuthorFrancis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen
Bioconductor views Genetics SomaticMutation
Date of publicationNone
MaintainerFrancis Blokzijl <F.Blokzijl@umcutrecht.nl>, Roel Janssen <R.R.E.Janssen-10@umcutrecht.nl>
LicenseMIT + file LICENSE
Version1.2.0
https://github.com/UMCUgenetics/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.

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

Functions

binomial_test Man page
enrichment_depletion_test Man page
extract_signatures Man page
fit_to_signatures Man page
genomic_distribution Man page
MutationalPatterns Man page
MutationalPatterns-package Man page
mutation_context Man page
mutations_from_vcf Man page
mutation_types Man page
mut_matrix Man page
mut_matrix_stranded Man page
mut_type_occurrences Man page
plot_192_profile Man page
plot_96_profile Man page
plot_compare_profiles Man page
plot_contribution Man page
plot_enrichment_depletion Man page
plot_rainfall Man page
plot_signature_strand_bias Man page
plot_spectrum Man page
plot_strand Man page
plot_strand_bias Man page
read_vcfs_as_granges Man page
strand_bias_test Man page
strand_from_vcf Man page
strand_occurrences Man page
type_context Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/Defunct.R R/MutationalPatterns.R R/binomial_test.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_matrix.R R/mut_matrix_stranded.R R/mut_type_occurrences.R R/mutation_context.R R/mutation_types.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_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_from_vcf.R R/strand_occurrences.R R/type_context.R
README.md
build
build/vignette.rds
images
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
inst/NEWS
inst/doc
inst/doc/Introduction_to_MutationalPatterns.R
inst/doc/Introduction_to_MutationalPatterns.Rnw
inst/doc/Introduction_to_MutationalPatterns.pdf
inst/extdata
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
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
man/MutationalPatterns-package.Rd man/binomial_test.Rd man/enrichment_depletion_test.Rd man/extract_signatures.Rd man/fit_to_signatures.Rd man/genomic_distribution.Rd man/mut_matrix.Rd man/mut_matrix_stranded.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_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
tests
tests/testthat
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
vignettes/Introduction_to_MutationalPatterns.Rnw
vignettes/references.bib

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

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