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cff-version: 1.2.0
message: 'To cite package "SmartPhos" in publications use:'
type: software
license: GPL-3.0-only
title: 'SmartPhos: A phosphoproteomics data analysis package with an interactive ShinyApp'
version: 1.3.0
doi: 10.32614/CRAN.package.SmartPhos
abstract: To facilitate and streamline phosphoproteomics data analysis, we developed
  SmartPhos, an R package for the pre-processing, quality control, and exploratory
  analysis of phosphoproteomics data generated by MaxQuant and Spectronaut. The package
  can be used either through the R command line or through an interactive ShinyApp
  called SmartPhos Explorer. The package contains methods such as normalization and
  normalization correction, transformation, imputation, batch effect correction, PCA,
  heatmap, differential expression, time-series clustering, gene set enrichment analysis,
  and kinase activity inference.
authors:
- family-names: Agrawal
  given-names: Shubham
  email: shubhamagrawal2706@gmail.com
  orcid: https://orcid.org/0009-0005-2630-9342
- family-names: Lu
  given-names: Junyan
  email: jylu1118@gmail.com
  orcid: https://orcid.org/0000-0002-9211-0746
repository: https://bioc.r-universe.dev
repository-code: https://github.com/Bioconductor/SmartPhos
commit: fbaec544efe26887f16c395fc1bffe524eb9fc18
url: https://lu-group-ukhd.github.io/SmartPhos/
date-released: '2026-04-28'
contact:
- family-names: Agrawal
  given-names: Shubham
  email: shubhamagrawal2706@gmail.com
  orcid: https://orcid.org/0009-0005-2630-9342