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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 "DEP" in publications use:'
type: software
license: Artistic-2.0
title: 'DEP: Differential Enrichment analysis of Proteomics data'
version: 1.27.0
abstract: This package provides an integrated analysis workflow for robust and reproducible
  analysis of mass spectrometry proteomics data for differential protein expression
  or differential enrichment. It requires tabular input (e.g. txt files) as generated
  by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant
  or IsobarQuant. Functions are provided for data preparation, filtering, variance
  normalization and imputation of missing values, as well as statistical testing of
  differentially enriched / expressed proteins. It also includes tools to check intermediate
  steps in the workflow, such as normalization and missing values imputation. Finally,
  visualization tools are provided to explore the results, including heatmap, volcano
  plot and barplot representations. For scientists with limited experience in R, the
  package also contains wrapper functions that entail the complete analysis workflow
  and generate a report. Even easier to use are the interactive Shiny apps that are
  provided by the package.
authors:
- family-names: Smits
  given-names: Arne
  email: smits.arne@gmail.com
- family-names: Huber
  given-names: Wolfgang
  email: wolfgang.huber@embl.de
preferred-citation:
  type: article
  title: Proteome-wide identification of ubiquitin interactions using UbIA-MS
  authors:
  - family-names: Zhang
    given-names: Xiaofei
  - family-names: Smits
    given-names: Arne H
  - family-names: Tilburg
    given-names: Gabrielle BA
    name-particle: van
  - family-names: Ovaa
    given-names: Huib
  - family-names: Huber
    given-names: Wolfgang
    email: wolfgang.huber@embl.de
  - family-names: Vermeulen
    given-names: Michiel
  journal: Nature Protocols
  year: '2018'
  volume: '13'
  start: 530–550
repository: https://bioc.r-universe.dev
contact:
- family-names: Smits
  given-names: Arne
  email: smits.arne@gmail.com