bio-expression-matrix-gene-id-mapping
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.
npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-id-mapping --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: pandas 2.2+ 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. # Gene ID Mapping ## Python: mygene **Goal:** Convert between gene identifier systems (Ensembl, Entrez, Symbol, UniProt) using the MyGene.info API. **Approach:** Query mygene with source IDs, specifying scopes and target fields, to build an ID mapping dictionary. **"Convert my Ensembl gene IDs to gene symbols"** → Query a gene annotation service to map between identifier systems, handling one-to-many mappings. ```python import mygene import pandas as pd mg = mygene.MyGeneInfo() # Ensembl to Symbol ensembl_ids = ['ENSG00000141510', 'ENSG00000012048', 'ENSG00000141736'] results = mg.querymany(ensembl_ids, scopes='ensembl.gene', fields='symbol', species='human') mapping = {r['query']: r.get('symbol', None) for r in results} # {'EN
- Version Compatibility
- Python: mygene
- Python: pyensembl
- Python: gseapy
- R: biomaRt
- R: org.db Packages
- Apply Mapping to Count Matrix
- R Equivalent
- Handle Unmapped IDs
- Common ID Types and Database Selection
- Database Selection Guide
- Gene Symbol Instability
- PAR Gene Complications
- Cross-Species Ortholog Mapping
What does the bio-expression-matrix-gene-id-mapping skill do?
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-id-mapping --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.