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Use this skill to run deterministic local custom enrichment with Bioconductor clusterProfiler and user-supplied TERM2GENE tables. Do not use it for remote annotation downloads or organism database lookups.
Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
SOC 직업 분류 기준
Use this skill to search the current ClinicalTrials.gov v2 API for condition or keyword matches when you need official clinical-study metadata. Do not use it for legacy API URLs or offline work.
Use this skill to resolve a gene symbol to Ensembl IDs and fetch a canonical Ensembl gene record. Do not use it for full transcript annotation pipelines or offline work.
Use this skill to search NCBI Gene by symbol and organism, then fetch compact official Entrez Gene summaries. Do not use it for variant interpretation, transcript-level modeling, or bulk offline annotation.
Use this skill to author and run a minimal Common Workflow Language CommandLineTool and one-step workflow with cwltool. Do not use it for containerized production execution or complex scatter/gather workflows.
Use this skill to run a minimal Nextflow workflow through the repo-managed Java and Nextflow prefix, either locally or on the Slurm cluster. Do not use it for containerized production pipelines.
Use this skill to verify the repo-managed nf-core tools install and retrieve a cleaned summary of available pipelines. Do not use it for interactive launch flows or full pipeline downloads.
| name | clusterprofiler-custom-enrichment |
| description | Use this skill to run deterministic local custom enrichment with Bioconductor clusterProfiler and user-supplied TERM2GENE tables. Do not use it for remote annotation downloads or organism database lookups. |
Run a compact over-representation analysis with local query genes, local TERM2GENE, and local TERM2NAME tables through Bioconductor clusterProfiler.
TERM2GENE TSV with columns term and geneTERM2NAME TSV with columns term and name--install-missingRscriptjsonliteclusterProfiler for package-backed executionexamples/toy_query_genes.txt, examples/toy_term2gene.tsv, and examples/toy_term2name.tsv.Rscript skills/systems-biology/clusterprofiler-custom-enrichment/scripts/run_clusterprofiler_custom_enrichment.R --lib-dir /tmp/bioc-skill-lib --install-missing --out clusterprofiler_summary.json.results for term, description, gene_ratio, p_adjust, and gene_ids.--describe-toy returns the expected toy gene and term counts.clusterProfiler: rerun with --install-missing --lib-dir <path>.gdtools or ggiraph build failures: install Cairo and FreeType development headers before retrying the Bioconductor stack.TERM2GENE.TERM2NAME table keys match the TERM2GENE term IDs exactly.Rscript skills/systems-biology/clusterprofiler-custom-enrichment/scripts/run_clusterprofiler_custom_enrichment.R --describe-toyfgsea-preranked-enrichmentreactome-identifiers-enrichment