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bio-flow-cytometry-fcs-handling

Maintainer FreedomIntelligence · Last updated April 1, 2026

Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.

OpenClawNanoClawAnalysisReproductionbio-flow-cytometry-fcs-handling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — immunoinformatics & flow cytometryread

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-flow-cytometry-fcs-handling

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • R: flowCore::read.FCS() or flowCore::read.flowSet() for multiple files.
  • Python: fcsparser.parse() or FlowCal.io.FCSData().
  • Load my FCS files into R or Python" → Read Flow Cytometry Standard (FCS) files, access channel parameters and metadata, and explore event data for downstream analysis. R: flowCore::read.FCS() or flowCore::read.flowSet() for multiple files Python: fcsparser.parse() or FlowCal.io.FCSData().
  • fcs <- read.FCS('sample.fcs', transformation = FALSE, truncate_max_range = FALSE).

Source Doc

Excerpt From SKILL.md

Load FCS Files

Goal: Read a single FCS file and inspect its parameters and metadata.

Approach: Use flowCore's read.FCS with transformation disabled to load raw data, then examine parameter names and descriptions.

library(flowCore)

## Parameter names

colnames(fcs)  # Short names
pData(parameters(fcs))  # Full metadata including descriptions

Load Multiple Files

Goal: Read a batch of FCS files into a single flowSet container for uniform processing.

Approach: List FCS files from a directory and load them into a flowSet with read.flowSet.

Use cases

  • Use when loading and inspecting flow or mass cytometry data before preprocessing.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • compensation-transformation - Apply compensation and transforms
  • gating-analysis - Define cell populations
  • clustering-phenotyping - Unsupervised analysis

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