https://github.com/helenalc/catalyst

Cytometry dATa anALYsis Tools
https://github.com/helenalc/catalyst

Last synced: about 1 year ago
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Cytometry dATa anALYsis Tools

• Host: GitHub
• URL: https://github.com/helenalc/catalyst
• Owner: HelenaLC
• Created: 2016-12-01T12:06:28.000Z (over 9 years ago)
• Default Branch: main
• Last Pushed: 2025-05-09T09:42:47.000Z (about 1 year ago)
• Last Synced: 2025-05-09T10:40:45.400Z (about 1 year ago)
• Language: R
• Homepage:
• Size: 130 MB
• Stars: 68
• Watchers: 11
• Forks: 31
• Open Issues: 16
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS

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README

          
# Welcome to `CATALYST` 

`CATALYST` leverages existing R/Bioconductor infrastructure by building around Biocondcutor's `SingleCellExperiment` class, and by providing an interface for conversion to other data structures established in the cytometry community (e.g., `flowCore`'s `flowFrame/Set` classes), thus facilitating communication with existing tools for visualization (e.g., `ggcyto`) and gating (e.g., `openCyto`).  The package currently provides:

- an extensive suit of visualizations for differential discovery

- a pipeline for preprocessing of cytometry data, including

  - normalization using bead standards

  - single-cell deconvolution

  - bead-based compensation

  

### References

- Chevrier S☆, Crowell HL☆, Zanotelli VRT☆, Engler S, Robinson MD & Bodenmiller B (2018):  

*Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry*. Cell Systems 6(5):612-620.e5. 

- Nowicka M, Krieg C, Crowell HL, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP & Robinson MD (2017):  

*CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets*. F1000Resaearch 6:748. 

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### Got a problem (or an idea)?

`CATALYST` is still under active development. We greatly welcome (and highly encourage!) all feedback, bug reports and suggestions for improvement [HERE](https://github.com/HelenaLC/CATALYST/issues). **Please make sure to raise issues with a reproducible example and the output of your `sessionInfo()`.**