MutationalPatterns: Studying patterns in base substitution catalogues

Share:

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

Author
Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen
Date of publication
None
Maintainer
Francis Blokzijl <F.Blokzijl@umcutrecht.nl>, Roel Janssen <R.R.E.Janssen-10@umcutrecht.nl>
License
MIT + file LICENSE
Version
1.0.0
URLs

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