bio-tcr-bcr-analysis-immcantation-analysis
Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework. Use when studying B cell affinity maturation, germinal center dynamics, or antibody evolution.
npx skills add majiayu000/claude-skill-registry --skill immcantation-analysis --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.
# Immcantation Analysis Requires Immcantation suite: alakazam 1.3+, shazam 1.2+, scoper 1.3+, dowser 2.0+, tigger 1.1+. ## Load and Format Data ```r library(alakazam) library(shazam) library(dplyr) # Load AIRR-formatted data (from MiXCR, IMGT/HighV-QUEST, etc.) db <- readChangeoDb('clones_airr.tsv') # Required columns: # sequence_id, sequence, v_call, d_call, j_call, junction, junction_aa ``` ## Clonal Clustering ```r library(scoper) # Assign clones based on junction similarity # Threshold typically 0.15-0.2 (15-20% nucleotide distance) db <- hierarchicalClones( db, threshold = 0.15, method = 'nt', linkage = 'single' ) # Count clones clone_sizes <- countClones(db, groups = 'sample_id') ``` ## Somatic Hypermutation Analysis ```r # Calculate mutation frequencies db <- observedMutations( db, sequenceColumn = 'sequence_alignment', germlineColumn = 'germline_alignment_d_mask', regionDefinition = IMGT_V, mutationDefinition = MUTATION_SCHEMES$S5F ) # Mutation frequency columns added: # mu_count_seq_r, mu_count_seq_s (replacement/silent mutations) # mu_freq_seq_r, mu_freq_seq_s (frequencies) # Summarize by clone mutation_summary <- db %>% group_by(clone_id) %>% summarize( mean_mu = mean(mu
- Load and Format Data
- Clonal Clustering
- Somatic Hypermutation Analysis
- Selection Analysis
- Build Clonal Lineage Trees
- Germline Inference
- Visualization
- Related Skills
What does the bio-tcr-bcr-analysis-immcantation-analysis skill do?
Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework. Use when studying B cell affinity maturation, germinal center dynamics, or antibody evolution.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill immcantation-analysis --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.