bio-metagenomics-functional-profiling
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-functional-profiling --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: HUMAnN 3.8+, MetaPhlAn 4.1+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, seaborn 0.13+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Functional Profiling **"What metabolic pathways are present in my metagenome?"** → Profile functional potential of metagenomic samples to obtain pathway abundances and gene family counts using translated search against UniRef and MetaCyc. - CLI: `humann --input reads.fastq --output results/` (HUMAnN3) Profile the functional potential of metagenomic samples using HUMAnN3 to get pathway and gene family abundances. ## HUMAnN3 Workflow ### Installation ```bash # Install via conda (recommended) conda create -n humann -c bioconda humann conda activate humann # Download databases humann_databases --download chocophlan full /path/to/databases humann_databas
- Version Compatibility
- HUMAnN3 Workflow
- Installation
- Basic Usage
- Output Files
- Output Format
- Gene Families
- Pathway Abundance
- Batch Processing
- Normalization
- Regroup Gene Families
- Stratification
- Split by Organism
- Species Contributions
Install via conda (recommended) conda create -n humann -c bioconda humann conda activate humann Download databases humann_databases --download chocophlan full /path/to/databases humann_databases --download uniref uniref90_diamond /path/to/databases Update config with database paths humann_config --update database_folders nucleotide /path/to/databases/chocophlan humann_config --update database_folders protein /path/to/databases/uniref Run HUMAnN3 on a single sample
What does the bio-metagenomics-functional-profiling skill do?
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-functional-profiling --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.