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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "ramwas" in publications use:'
type: software
license: LGPL-3.0-only
title: 'ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms'
version: 1.29.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ramwas
abstract: 'A complete toolset for methylome-wide association studies (MWAS). It is
  specifically designed for data from enrichment based methylation assays, but can
  be applied to other data as well. The analysis pipeline includes seven steps: (1)
  scanning aligned reads from BAM files, (2) calculation of quality control measures,
  (3) creation of methylation score (coverage) matrix, (4) principal component analysis
  for capturing batch effects and detection of outliers, (5) association analysis
  with respect to phenotypes of interest while correcting for top PCs and known covariates,
  (6) annotation of significant findings, and (7) multi-marker analysis (methylation
  risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis
  of methlyation and genotype data. This work is published in Bioinformatics, Shabalin
  et al. (2018) <https://doi.org/10.1093/bioinformatics/bty069>.'
authors:
- family-names: Shabalin
  given-names: Andrey A
  email: andrey.shabalin@gmail.com
  orcid: https://orcid.org/0000-0003-0309-6821
- family-names: Clark
  given-names: Shaunna L
  email: slclark2@vcu.edu
- family-names: Hattab
  given-names: Mohammad W
  email: mwhattab@vcu.edu
- family-names: Aberg
  given-names: Karolina A
  email: kaaberg@vcu.edu
- family-names: Oord
  given-names: Edwin J C G
  name-particle: van den
  email: ejvandenoord@vcu.edu
preferred-citation:
  type: article
  title: 'RaMWAS: fast methylome-wide association study pipeline for enrichment platforms'
  authors:
  - family-names: Shabalin
    given-names: Andrey A
    email: andrey.shabalin@gmail.com
    orcid: https://orcid.org/0000-0003-0309-6821
  - family-names: Hattab
    given-names: Mohammad W
    email: mwhattab@vcu.edu
  - family-names: Clark
    given-names: Shaunna L
    email: slclark2@vcu.edu
  - family-names: Chan
    given-names: Robin F
  - family-names: Kumar
    given-names: Gaurav
  - family-names: Aberg
    given-names: Karolina A
    email: kaaberg@vcu.edu
  - family-names: Oord
    given-names: Edwin JCG
    name-particle: van den
  year: '2018'
  url: http://dx.doi.org/10.1093/bioinformatics/bty069
  publisher:
    name: Oxford University Press
  journal: Bioinformatics
repository: https://bioc.r-universe.dev
repository-code: https://github.com/andreyshabalin/ramwas
commit: 4914fc53c9addd690b228fe61f6f2686f0de6a0f
url: https://bioconductor.org/packages/ramwas/
date-released: '2019-02-18'
contact:
- family-names: Shabalin
  given-names: Andrey A
  email: andrey.shabalin@gmail.com
  orcid: https://orcid.org/0000-0003-0309-6821