# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "MutationalPatterns" in publications use:'
type: software
license: MIT
title: 'MutationalPatterns: Comprehensive genome-wide analysis of mutational processes'
version: 3.15.0
doi: 10.1186/s12864-022-08357-3
identifiers:
- type: doi
  value: 10.32614/CRAN.package.MutationalPatterns
abstract: 'Mutational processes leave characteristic footprints in genomic DNA. This
  package provides a comprehensive set of flexible functions that allows researchers
  to easily evaluate and visualize a multitude of mutational patterns in base substitution
  catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells.
  The package covers a wide range of patterns including: mutational signatures, transcriptional
  and replicative strand bias, lesion segregation, genomic distribution and association
  with genomic features, which are collectively meaningful for studying the activity
  of mutational processes. The package works with single nucleotide variants (SNVs),
  insertions and deletions (Indels), double base substitutions (DBSs) and larger multi
  base substitutions (MBSs). The package provides functionalities for both extracting
  mutational signatures de novo and determining the contribution of previously identified
  mutational signatures on a single sample level. MutationalPatterns integrates with
  common R genomic analysis workflows and allows easy association with (publicly available)
  annotation data.'
authors:
- family-names: Manders
  given-names: Freek
  email: F.M.Manders@prinsesmaximacentrum.nl
  orcid: https://orcid.org/0000-0001-6197-347X
- family-names: Blokzijl
  given-names: Francis
  orcid: https://orcid.org/0000-0002-8084-8444
- family-names: Janssen
  given-names: Roel
  orcid: https://orcid.org/0000-0003-4324-5350
- family-names: Roosmalen
  given-names: Mark
  name-particle: van
  email: vanBoxtelBioinformatics@prinsesmaximacentrum.nl
- family-names: Boxtel
  given-names: Ruben
  name-particle: van
  orcid: https://orcid.org/0000-0003-1285-2836
- family-names: Cuppen
  given-names: Edwin
  orcid: https://orcid.org/0000-0002-0400-9542
preferred-citation:
  type: article
  title: 'MutationalPatterns: The one stop shop for the analysis of mutational processes'
  authors:
  - family-names: Manders
    given-names: Freek
    email: F.M.Manders@prinsesmaximacentrum.nl
    orcid: https://orcid.org/0000-0001-6197-347X
  - family-names: Brandsma
    given-names: Arianne M.
  - family-names: Kanter
    given-names: Jurrian
    name-particle: de
  - family-names: Verheul
    given-names: Mark
  - family-names: Oka
    given-names: Rurika
  - family-names: Roosmalen
    given-names: Markus J.
    name-particle: van
  - family-names: Roest
    given-names: Bastiaan
    name-particle: van der
  - family-names: Hoeck
    given-names: Arne
    name-particle: van
  - family-names: Cuppen
    given-names: Edwin
    orcid: https://orcid.org/0000-0002-0400-9542
  - family-names: Boxtel
    given-names: Ruben
    name-particle: van
    orcid: https://orcid.org/0000-0003-1285-2836
  year: '2022'
  journal: BMC Genomics
  doi: 10.1186/s12864-022-08357-3
repository: https://bioc.r-universe.dev
commit: 3141f4438f9973b2e599872d3f4bc615b117169d
url: https://doi.org/doi:10.1186/s12864-022-08357-3
date-released: '2024-04-05'
contact:
- family-names: Roosmalen
  given-names: Mark
  name-particle: van
  email: vanBoxtelBioinformatics@prinsesmaximacentrum.nl