bio-flow-cytometry-cytometry-qc
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying problematic samples before analysis.
npx skills add majiayu000/claude-skill-registry --skill cytometry-qc --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.
# Cytometry QC ## Automated QC with flowAI ```r library(flowAI) library(flowCore) # Load FCS file ff <- read.FCS('sample.fcs') # Run automated QC # Checks: flow rate, signal stability, dynamic range qc_result <- flow_auto_qc( ff, folder_results = 'qc_output/', fcs_QC = TRUE, # Export QC'd FCS html_report = TRUE, # Generate HTML report mini_report = TRUE # Also make summary ) # Get cleaned data ff_clean <- qc_result$fcs # QC metrics cat('Original events:', nrow(ff), '\n') cat('After QC:', nrow(ff_clean), '\n') cat('Removed:', nrow(ff) - nrow(ff_clean), '(', round((1 - nrow(ff_clean)/nrow(ff)) * 100, 1), '%)\n') ``` ## Flow Rate Stability ```r # Check for acquisition issues via flow rate check_flow_rate <- function(ff, time_channel = 'Time') { expr <- exprs(ff) time <- expr[, time_channel] # Bin by time n_bins <- 50 bins <- cut(time, breaks = n_bins, labels = FALSE) # Events per bin (flow rate proxy) events_per_bin <- table(bins) flow_rate <- as.numeric(events_per_bin) # Calculate metrics cv <- sd(flow_rate) / mean(flow_rate) * 100 # Detect anomalies (>2 SD from mean) z_scores <- abs(scale(flow_rate)) anomalies <- which(z_scores > 2) list( mean_rate = mean(flow_rate), cv_percent = cv
- Automated QC with flowAI
- Flow Rate Stability
- Signal Drift Detection
- Margin Events Removal
- Dead Cell Exclusion
- CyTOF-Specific QC
- Batch QC Summary
- Visualization
- QC Report Generation
- Related Skills
What does the bio-flow-cytometry-cytometry-qc skill do?
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying problematic samples before analysis.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill cytometry-qc --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 majiayu000/claude-skill-registry, a repository with 534 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.