bio-flow-cytometry-bead-normalization
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing data across batches.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-flow-cytometry-bead-normalization --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+, ggplot2 3.5+ 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. # Bead Normalization **"Normalize my CyTOF data using beads"** → Correct instrument signal drift over acquisition time using EQ calibration bead intensities for consistent measurements across runs. - R: `CATALYST::normCytof()` for EQ bead normalization ## CyTOF EQ Bead Normalization **Goal:** Identify EQ normalization bead events in CyTOF data for signal calibration. **Approach:** Score events by mean scaled intensity in known bead channels (Ce140, Eu151, Eu153, Ho165, Lu175) and threshold at the 99th percentile. ```r library(CATALYST) library(flowCore) # CyTOF data typically includes EQ normalization beads # Fluidigm provides normalizer software, but can also do in R # Load FCS with beads ff <- read.FCS('cytof_with_beads.fcs') # EQ beads contain known amounts of: Ce140, Eu151, Eu153, Ho16
- Version Compatibility
- CyTOF EQ Bead Normalization
- Calculate Normalization Factors
- Apply Normalization
- Time-Based Drift Correction
- Batch Normalization with CytoNorm
- Quantile Normalization
- CATALYST-Based Normalization
- Visualization
- Export Normalized Data
- Related Skills
What does the bio-flow-cytometry-bead-normalization skill do?
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing data across batches.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-flow-cytometry-bead-normalization --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.