# --------------------------------------------
# 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 "pmartR" in publications use:'
type: software
license: BSD-2-Clause
title: 'pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for
  Panomics Data'
version: 2.4.6
doi: 10.1021/acs.jproteome.2c00610
identifiers:
- type: doi
  value: 10.32614/CRAN.package.pmartR
abstract: 'Provides functionality for quality control processing and statistical analysis
  of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide
  or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based
  count data and nuclear magnetic resonance (NMR) data. This includes data transformation,
  specification of groups that are to be compared against each other, filtering of
  features and/or samples, data normalization, data summarization (correlation, PCA),
  and statistical comparisons between defined groups. Implements methods described
  in: Webb-Robertson et al. (2014) <https://doi.org/10.1074/mcp.M113.030932>. Webb-Robertson
  et al. (2011) <https://doi.org/10.1002/pmic.201100078>. Matzke et al. (2011) <https://doi.org/10.1093/bioinformatics/btr479>.
  Matzke et al. (2013) <https://doi.org/10.1002/pmic.201200269>. Polpitiya et al.
  (2008) <https://doi.org/10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010)
  <https://doi.org/10.1021/pr1005247>.'
authors:
- family-names: Bramer
  given-names: Lisa
  email: lisa.bramer@pnnl.gov
- family-names: Stratton
  given-names: Kelly
  email: kelly.stratton@pnnl.gov
- family-names: Claborne
  given-names: Daniel
  email: daniel.claborne@pnnl.gov
preferred-citation:
  type: article
  title: 'pmartR 2.0: A Quality Control, Visualization, and Statistics Pipeline for
    Multiple Omics Datatypes'
  authors:
  - family-names: Degnan
    given-names: David
    email: david.degnan@pnnl.gov
  - family-names: Stratton
    given-names: Kelly
    email: kelly.stratton@pnnl.gov
  - family-names: Richardson
    given-names: Rachel
    email: rachel.richardson@pnnl.gov
  - family-names: Claborne
    given-names: Daniel
    email: daniel.claborne@pnnl.gov
  - family-names: Martin
    given-names: Evan
  - family-names: Johnson
    given-names: Nathan
  - family-names: Leach
    given-names: Damon
    email: damon.leach@pnnl.gov
  - family-names: Webb-Robertson
    given-names: Bobbie-Jo
  - family-names: Bramer
    given-names: Lisa
    email: lisa.bramer@pnnl.gov
  journal: Journal of Proteome Research
  year: '2023'
  volume: '22'
  issue: '2'
  doi: 10.1021/acs.jproteome.2c00610
  start: 570-576
repository: https://CRAN.R-project.org/package=pmartR
repository-code: https://github.com/pmartR/pmartR
url: https://pmartr.github.io/pmartR/
date-released: '2024-10-08'
contact:
- family-names: Bramer
  given-names: Lisa
  email: lisa.bramer@pnnl.gov
references:
- type: article
  title: 'pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological
    Data'
  authors:
  - family-names: Stratton
    given-names: Kelly
    email: kelly.stratton@pnnl.gov
  - family-names: Webb-Robertson
    given-names: Bobbie-Jo
  - family-names: McCue
    given-names: Lee Ann
  - family-names: Stanfill
    given-names: Bryan
  - family-names: Claborne
    given-names: Daniel
    email: daniel.claborne@pnnl.gov
  - family-names: Gomez
    given-names: Iobani
  - family-names: Johansen
    given-names: Thomas
  - family-names: Thompson
    given-names: Allison
  - family-names: Burnum-Johnson
    given-names: Kristin
  - family-names: Waters
    given-names: Katrina
  - family-names: Bramer
    given-names: Lisa
    email: lisa.bramer@pnnl.gov
  journal: Journal of Proteome Research
  year: '2019'
  volume: '18'
  issue: '3'
  doi: 10.1021/acs.jproteome.8b00760
  start: 1418-1425