# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "puma" in publications use:'
type: software
license: LGPL-2.0-only
title: 'puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix
  tranditional 3'' arrays and exon arrays and Human Transcriptome Array 2.0)'
version: 3.47.0
abstract: Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays
  and exon arrays and Human Transcriptome Array 2.0) are based on point estimates
  of expression levels and ignore the uncertainty of such estimates. By propagating
  uncertainty to downstream analyses we can improve results from microarray analyses.
  For the first time, the puma package makes a suite of uncertainty propagation methods
  available to a general audience. In additon to calculte gene expression from Affymetrix
  3' arrays, puma also provides methods to process exon arrays and produces gene and
  isoform expression for alternative splicing study. puma also offers improvements
  in terms of scope and speed of execution over previously available uncertainty propagation
  methods. Included are summarisation, differential expression detection, clustering
  and PCA methods, together with useful plotting functions.
authors:
- family-names: Liu
  given-names: Xuejun
  email: xuejun.liu@nuaa.edu.cn
- family-names: Pearson
  given-names: Richard D.
- family-names: Rattray
  given-names: Magnus
- family-names: Milo
  given-names: Marta
- family-names: Lawrence
  given-names: Neil D.
- family-names: Sanguinetti
  given-names: Guido
- family-names: Zhang
  given-names: Li
preferred-citation:
  type: article
  title: 'puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis'
  authors:
  - family-names: al
    given-names: Pearson et
  journal: in preparation
  year: '2008'
repository: https://bioc.r-universe.dev
url: http://umber.sbs.man.ac.uk/resources/puma
date-released: '2015-07-29'
contact:
- family-names: Liu
  given-names: Xuejun
  email: xuejun.liu@nuaa.edu.cn
references:
- type: article
  title: 'puma3.0: improved uncertainty propagation methods for gene and transcirpt
    expression and analysis.'
  authors:
  - family-names: Zhang
    given-names: Xuejun Liu,Zhenzhu Gao,Li
  journal: BMC Bioinformatics
  year: '2013'
- type: generic
  title: ANSI-C version of donlp2()
  authors:
  - family-names: Spelluci
    given-names: P.
  medium: http://plato.asu.edu/ftp/donlp2/donlp2_intv_dyn.tar.gz