Beta release v0.2.1

Publication Notice

We are pleased to announce that GatingTree: Pathfinding Analysis of Group-Specific Effects in Cytometry Data has been accepted and published in Cytometry Part A (July 2025) by Wiley.

Ono, M. (2025). GatingTree: Pathfinding Analysis of Group-Specific Effects in Cytometry Data. Cytometry Part A, 107(7), 476–496. https://doi.org/10.1002/cyto.a.24948

You can now cite GatingTree directly:

• APA:

  Ono, M. (2025). GatingTree: Pathfinding Analysis of Group-Specific Effects in Cytometry Data. Cytometry Part A, 107(7), 476–496. https://doi.org/10.1002/cyto.a.24948

• BibTeX:

  @article{ono2025gatingtree,
    author       = {Ono, Masahiro},
    title        = {GatingTree: Pathfinding Analysis of Group-Specific Effects in Cytometry Data},
    journal      = {Cytometry Part A},
    volume       = {107},
    number       = {7},
    pages        = {476--496},
    year         = {2025},
    doi          = {10.1002/cyto.a.24948},
    month        = jul
  }

Version 0.2.0 (beta)

• New Features Included:
  • GatingTreeRandomForest: New function to apply Random Forest analysis to GatingTree node data.
  • predictGatingTreeRandomForest: New function to perform predictions using models built with GatingTreeRandomForest.
  • AnalyzeNodeOverlaps: New function to analyze the percentage of cells shared between nodes, aiding in the unsupervised analysis of GatingTree node data.
  • ExtractTopNodes: New function designed to extract top nodes from node clusters, enhancing the unsupervised approach in node analysis.

v0.1.1-beta

This version improves the function PlotDeltaEnrichment and added a new function, PlotDeltaEnrichmentPrunedTree, which unravels the impacts of key markers.

Beta release of GatingTree

v0.1.0-beta

We are excited to announce the first beta release of the GatingTree package!

This version introduces a variety of tools designed to enhance the analysis of group-specific effects in cytometry data through pathfinding analysis that does not rely on traditional dimensional reduction techniques.

For more details on the package's capabilities and how to get started, please visit our documentation site:
https://monotockylab.github.io/GatingTree/