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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-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.
## Version Compatibility Reference examples tested with: MiXCR 4.6+, 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. # Immcantation Analysis **"Analyze B cell repertoire evolution and clonal lineages"** → Study somatic hypermutation, build B cell phylogenies, and track affinity maturation using the Immcantation framework for BCR repertoire analysis. - R: `alakazam::plotMutability()`, `dowser::buildPhylipLineage()`, `scoper::spectralClones()` Requires Immcantation suite: alakazam 1.3+, shazam 1.2+, scoper 1.3+, dowser 2.0+, tigger 1.1+. ## Load and Format Data **Goal:** Import AIRR-formatted repertoire data into the Immcantation framework for downstream analysis. **Approach:** Read Change-O/AIRR tab-delimited files into R data frames with required V(D)J annotation columns. ```r library(alakazam) library(shazam) library(dplyr) # Load AIRR-formatted data (from MiXCR, IMGT/HighV-QUEST, etc.) db <- readChangeoDb(
- Version Compatibility
- 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-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 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.