CytoML

CytoML enables standardized, cross-platform import, manipulation, and export of gated cytometry data to interoperate between commercial platforms (FlowJo, Cytobank, BD FACSDiva) and R/Bioconductor analytical workflows.

Key Features:

• Cross-platform import/export: Reads and writes gating hierarchies and compensated/normalized cytometry measurements across FlowJo, Cytobank, and BD FACSDiva.
• Complete gating structure import: Imports gates, transformations, compensation matrices, and population hierarchies directly into R for downstream analysis.
• Bidirectional exchange: Exports modified or newly generated gating strategies back to FlowJo and Cytobank.
• Mass cytometry support: Imports gated mass cytometry datasets from Cytobank to enable combined analyses of flow and mass cytometry.
• Integration with Bioconductor: Integrates with R/Bioconductor packages to combine gating-based approaches with algorithmic methods, high-dimensional clustering, and downstream statistical modeling.
• Standardized representations: Provides standardized, manipulable representations of gating structures to enable interoperability between proprietary software and open-source workflows in R.

Scientific Applications:

• Reproducibility and standardization: Enables validation of reproducibility and standardization of cytometry analyses across laboratories.
• Cross-platform analyses: Supports comparative and integrative analyses spanning flow and mass cytometry datasets.
• Hybrid analysis workflows: Facilitates combining manual gating with algorithmic methods, high-dimensional clustering, and downstream statistical modeling.
• Data sharing and collaboration: Enables exchange of gated cytometry data between computational analysts and bench scientists for collaborative workflows.

Methodology:

Reading and writing gating hierarchies; importing and exporting gates, transformations, compensation matrices, and population hierarchies; handling compensated/normalized cytometry measurements; importing gated mass cytometry datasets from Cytobank; and exporting gating strategies to FlowJo and Cytobank, with integration points for R/Bioconductor packages.