pcaExplorer

pcaExplorer is an R tool to analyze and interactively visualize RNA-seq datasets. The pcaExplorer algorithm uses Principal component analysis (PCA).

Topic

Data visualisation;RNA-Seq;Sequencing;Gene expression

Detail

  • Operation: Principal component plotting

  • Software interface: Command-line user interface

  • Language: R (Shiny)

  • License: The MIT licence

  • Cost: Free

  • Version name: 2.24.0

  • Credit: German Federal Ministry of Education and Research (BMBF).

  • Input: -

  • Output: -

  • Contact: Federico Marini marinif@uni-mainz.de

  • Collection: -

  • Maturity: Stable

Publications

  • Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, Ideal, and GeneTonic
  • Ludt A, Ustjanzew A, Binder H, Strauch K, Marini F. Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, Ideal, and GeneTonic. Curr Protoc. 2022 Apr;2(4):e411. doi: 10.1002/cpz1.411. PMID: 35467799.
  • https://doi.org/10.1002/cpz1.411
  • PMID: 35467799
  • PMC: -
  • pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
  • Marini F, Binder H. pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components. BMC Bioinformatics. 2019 Jun 13;20(1):331. doi: 10.1186/s12859-019-2879-1. PMID: 31195976; PMCID: PMC6567655.
  • https://doi.org/10.1186/s12859-019-2879-1
  • PMID: 31195976
  • PMC: PMC6567655

Download and documentation

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