bio-tcr-bcr-analysis-repertoire-visualization
Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Use when generating figures for repertoire comparisons, clonal dynamics, or V(D)J gene usage.
npx skills add majiayu000/claude-skill-registry --skill repertoire-visualization-gptomics-bioskills --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.
# Repertoire Visualization ## Circos Plots (V-J Gene Usage) ### VDJtools ```bash # Generate V-J usage circos plot vdjtools PlotFancyVJUsage \ -m metadata.txt \ output_dir/ # Generates PDF circos plots showing V-J pairing frequencies ``` ### Python with pyCircos ```python import pandas as pd import matplotlib.pyplot as plt from pycircos import Gcircle def plot_vj_circos(clone_df): '''Create circos plot of V-J usage''' # Count V-J pairs vj_counts = clone_df.groupby(['v_gene', 'j_gene']).size().reset_index(name='count') # Create circos circle = Gcircle() # Add arcs for each V and J gene v_genes = vj_counts['v_gene'].unique() j_genes = vj_counts['j_gene'].unique() # Add sectors and links # ... (complex setup) circle.save('vj_circos.pdf') ``` ### R with circlize ```r library(circlize) plot_vj_circos <- function(clone_df) { # Prepare adjacency matrix vj_matrix <- table(clone_df$v_gene, clone_df$j_gene) # Create circos plot chordDiagram( vj_matrix, transparency = 0.5, annotationTrack = c("grid", "name") ) } ``` ## Clone Tracking Over Time ```python import pandas as pd import matplotlib.pyplot as plt def plot_clone_tracking(clones_by_time, top_n=10): '''Track top clones across timepoints''
- Circos Plots (V-J Gene Usage)
- VDJtools
- Python with pyCircos
- R with circlize
- Clone Tracking Over Time
- Diversity Plots
- Overlap Heatmap
- Spectratype Plot
- Clonotype Network
- Related Skills
Generate V-J usage circos plot vdjtools PlotFancyVJUsage \ output_dir/ Generates PDF circos plots showing V-J pairing frequencies
What does the bio-tcr-bcr-analysis-repertoire-visualization skill do?
Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Use when generating figures for repertoire comparisons, clonal dynamics, or V(D)J gene usage.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill repertoire-visualization-gptomics-bioskills --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.