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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 "missMethyl" in publications use:'
type: software
license: GPL-2.0-only
title: 'missMethyl: Analysing Illumina HumanMethylation BeadChip Data'
version: 1.39.13
abstract: Normalisation, testing for differential variability and differential methylation
  and gene set testing for data from Illumina's Infinium HumanMethylation arrays.
  The normalisation procedure is subset-quantile within-array normalisation (SWAN),
  which allows Infinium I and II type probes on a single array to be normalised together.
  The test for differential variability is based on an empirical Bayes version of
  Levene's test. Differential methylation testing is performed using RUV, which can
  adjust for systematic errors of unknown origin in high-dimensional data by using
  negative control probes. Gene ontology analysis is performed by taking into account
  the number of probes per gene on the array, as well as taking into account multi-gene
  associated probes.
authors:
- family-names: Phipson
  given-names: Belinda
  email: phipson.b@wehi.edu.au
- family-names: Maksimovic
  given-names: Jovana
  email: jovana.maksimovic@petermac.org
preferred-citation:
  type: article
  title: 'SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450
    BeadChips'
  authors:
  - family-names: Maksimovic
    given-names: Jovana
    email: jovana.maksimovic@petermac.org
  - family-names: Gordon
    given-names: Lavinia
  - family-names: Oshlack
    given-names: Alicia
  journal: Genome Biology
  volume: '13'
  issue: '6'
  year: '2012'
  start: R44
repository: https://bioc.r-universe.dev
date-released: '2020-09-16'
contact:
- family-names: Phipson
  given-names: Belinda
  email: phipson.b@wehi.edu.au
- family-names: Maksimovic
  given-names: Jovana
  email: jovana.maksimovic@petermac.org
references:
- type: article
  title: 'DiffVar: A new method for detecting differential variability with application
    to methylation in cancer and aging'
  authors:
  - family-names: Phipson
    given-names: Belinda
  - family-names: Oshlack
    given-names: Alicia
  journal: Genome Biology
  volume: '15'
  issue: '9'
  year: '2014'
  start: '465'
- type: article
  title: Removing unwanted variation in a differential methylation analysis of Illumina
    HumanMethylation450 array data
  authors:
  - family-names: Maksimovic
    given-names: Jovana
  - family-names: Gagnon-Bartsch
    given-names: Johann A
  - family-names: Speed
    given-names: Terence P
  - family-names: Oshlack
    given-names: Alicia
  journal: Nucleic acids research
  year: '2015'
  start: gkv526
- type: article
  title: 'missMethyl: an R package for analysing methylation data from Illuminas HumanMethylation450
    platform'
  authors:
  - family-names: Phipson
    given-names: Belinda
  - family-names: Maksimovic
    given-names: Jovana
  - family-names: Oshlack
    given-names: Alicia
  journal: Bioinformatics
  year: '2015'
  start: btv560