bio-flow-cytometry-compensation-transformation
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-flow-cytometry-compensation-transformation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: flowCore 2.14+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Compensation and Transformation **"Compensate and transform my flow cytometry data"** → Correct spectral overlap between fluorophores using a compensation matrix and apply biexponential/arcsinh transforms for visualization and analysis. - R: `flowCore::compensate()` then `flowCore::transform()` with `estimateLogicle()` ## Load Compensation Matrix ```r library(flowCore) # From FCS file keywords fcs <- read.FCS('sample.fcs', transformation = FALSE) comp_matrix <- keyword(fcs)$`$SPILLOVER` # Or from CSV file comp_matrix <- as.matrix(read.csv('compensation.csv', row.names = 1)) ``` ## Apply Compensation ```r # Create compensation object comp <- compensation(comp_matrix) # Apply to flowFrame fcs_comp <- compensate(fcs, comp) # Apply to flowSet fs_comp <- compensate(fs, comp) ``` ## Calculate
- Version Compatibility
- Load Compensation Matrix
- Apply Compensation
- Calculate Compensation from Controls
- Transformation: Biexponential (Logicle)
- Transformation: Arcsinh (CyTOF)
- Transformation: Log
- View Before/After Compensation
- Complete Preprocessing Pipeline
- CATALYST Preprocessing (CyTOF)
- Panel File Format (CATALYST)
- Save Preprocessed Data
- Related Skills
What does the bio-flow-cytometry-compensation-transformation skill do?
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-flow-cytometry-compensation-transformation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.