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Gene identifier conversion between Ensembl, Entrez, HGNC symbols, and UniProt for bulk RNA-seq count matrices.
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インストールを決める前に、SKILL.md と SkillsMP に表示されている付属ファイルをお読みください。
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直接コマンドでは確認用 Prompt が省略されます。実行前にソースを確認してください。
npx skills add https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- --skill bulkrna-geneid-mappingコマンドは1行のまま表示されます。コピー前に横へスクロールして全体を確認してください。
ローカルで確認しますか？SkillsMP が現在取得できるファイルをダウンロードできます。
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SKILL.md を表示中
| name | bulkrna-geneid-mapping |
| description | Gene identifier conversion between Ensembl, Entrez, HGNC symbols, and UniProt for bulk RNA-seq count matrices. |
| version | 0.3.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["bulkrna","gene-id","mapping","Ensembl","Entrez","HGNC","annotation"] |
| requires | ["numpy","pandas"] |
| metadata | {"omicsclaw":{"domain":"bulkrna","emoji":"🏷️","trigger_keywords":["gene ID","Ensembl","Entrez","gene symbol","ID mapping","gene annotation","convert IDs"],"allowed_extra_flags":["--from","--mapping-file","--on-duplicate","--species","--to"],"legacy_aliases":["bulk-geneid"],"saves_h5ad":false}} |
Convert gene identifiers in bulk RNA-seq count matrices between major ID systems: Ensembl Gene IDs, Entrez Gene IDs, HGNC Symbols, and UniProt accessions. Features built-in mapping tables with optional mygene API fallback.
| Type | Example | Common Use |
|---|---|---|
| Ensembl Gene | ENSG00000141510 | RNA-seq quantification, GTF annotation |
| Entrez Gene | 7157 | NCBI databases, KEGG pathways |
| HGNC Symbol | TP53 | Human-readable, publications |
| UniProt | P04637 | Protein databases |
| Format | Extension | Description |
|---|---|---|
| Count matrix | .csv | Genes as rows (any ID type), samples as columns |
| Mapping table | .tsv |
Optional custom mapping: from_id, to_id columns |
python omicsclaw.py run bulkrna-geneid-mapping --demo
python omicsclaw.py run bulkrna-geneid-mapping --input counts.csv --from ensembl --to symbol --output results/
python bulkrna_geneid_mapping.py --demo --output /tmp/geneid_demo
output_directory/
├── report.md
├── result.json
├── tables/
│ ├── mapped_counts.csv
│ ├── mapping_table.csv
│ └── unmapped_genes.csv
└── reproducibility/
└── commands.sh
| Parameter | Default | Description |
|---|---|---|
--input | — | Path to count matrix CSV |
--from | ensembl | Source ID type: ensembl, entrez, symbol |
--to | symbol | Target ID type: ensembl, entrez, symbol |
--species | human | Species: human or mouse |
--mapping-file | — | Optional custom mapping TSV |
--on-duplicate | sum | Duplicate handling: sum, first, drop |
Chaining partners:
bulkrna-qc — Upstream: count matrix QCbulkrna-de — Downstream: DE analysis with harmonized IDsbulkrna-enrichment — Downstream: pathway enrichment requires specific ID typesRequired: numpy, pandas Optional: mygene (for API-based mapping when built-in tables insufficient)
bulkrna-qc — Count matrix QC upstreambulkrna-de — Differential expression downstreambulkrna-enrichment — Pathway enrichment (often requires Entrez IDs)