Flow cytometry analysis tools, oxidized. The aim of this workspace is to leverage the blazing-fast speed, memory and type safety, and fearless concurrency of the Rust language to scale-up to modern flow cytometry workflows requiring millions of events without breaking a sweat. Biological data can be unpredictable; the tools to analyze it shouldn't be.
The workspace includes libaries for:
- Reading FCS files
- Creating plots
- Working with gates
- QC'ing data
- Performing unmixing
🚧
⚠️ Under Construction: This workspace is actively under development. APIs may change, and some features may be incomplete. Use with caution in production environments.
🚧
This workspace contains multiple crates for flow cytometry analysis:
flow-fcs: A comprehensive, type-safe API for reading, parsing, and manipulating Flow Cytometry Standard (FCS) files. Built on top of Polars for efficient columnar data operations, with zero-copy data access, SIMD-accelerated operations, and support for common flow cytometry data transformations.flow-plots: Package for drawing and interacting with plots in flow cytometry data.flow-gates: Package for drawing and interacting with gates in flow cytometry data.peacoqc-rs: A reimplementation of the PeacoQC (R) algorithm from the Saeys lab, parallelized in Rust.peacoqc-cli: A command-line interface (CLI) tool for usingpeacoqc-rs.flow-tru-ols: TRU-OLS (Truncated ReUnmixing OLS) algorithm for flow cytometry unmixing; optional integration withflow-fcsandflow-plots.tru-ols-cli: Command-line tool for TRU-OLS unmixing (batch or single-file, with optional QC and plot output).
Contributions are welcome! Please feel free to submit a Pull Request or feature request.
This project is licensed under the MIT License - see the LICENSE file for details.