bio-epidemiological-genomics-transmission-inference
Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-transmission-inference --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: BioPython 1.83+, TreeTime 0.11+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - 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. # Transmission Inference **"Infer who infected whom in my outbreak"** → Reconstruct transmission networks from genomic and epidemiological data to identify transmission pairs, superspreaders, and unsampled cases. - R: `TransPhylo::inferTTree()` for Bayesian transmission tree inference ## TransPhylo in R ```r library(TransPhylo) library(ape) # Load dated phylogeny (from BEAST/TreeTime) tree <- read.nexus('dated_tree.nexus') # Convert to TransPhylo format ptree <- ptreeFromPhylo(tree, dateLastSample = 2020.5) # Estimate transmission tree # Uses MCMC to sample from posterior distribution res <- inferTTree( ptree, mcmcIterations = 100000, startNeg = 0.1, #
- Version Compatibility
- TransPhylo in R
- Prepare Data
- Interpret Results
- Python Alternative: outbreaker2 Wrapper
- Network Visualization
- Superspreader Analysis
- Related Skills
What does the bio-epidemiological-genomics-transmission-inference skill do?
Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-transmission-inference --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.