# Welcome to `CATALYST` <img src="inst/extdata/sticker.png" width="200" align="right" /> `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^&#9734;, Crowell HL^&#9734;, Zanotelli VRT^&#9734;, 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. --- ### 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()`.**