domains / families / science / fcs-handling

fcs-handling

separate

Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.

When to use

• loading flow or mass cytometry data
• mapping detector channels to antibodies
• extracting the event matrix
• choosing a reader
• bridging FCS to the scanpy/AnnData ecosystem
• parsing FlowJo/Cytobank/Diva workspaces
• inspecting FCS 2.0/3.0/3.1/3.2 internals
• accessing compensation matrices

Skill page

Source