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Use this skill to run deterministic toy or local custom preranked gene-set enrichment with Bioconductor fgsea. Do not use it for remote annotation lookups or large cohort-scale pathway workflows.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
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 | fgsea-preranked-enrichment |
| description | Use this skill to run deterministic toy or local custom preranked gene-set enrichment with Bioconductor fgsea. Do not use it for remote annotation lookups or large cohort-scale pathway workflows. |
Run preranked enrichment with a local ranked-statistics table and local pathway definitions through Bioconductor fgsea.
gene and scorepathway and gene--install-missingRscriptjsonlitefgsea for package-backed executionexamples/toy_ranked_stats.tsv and examples/toy_pathways.tsv.Rscript skills/systems-biology/fgsea-preranked-enrichment/scripts/run_fgsea_preranked.R --lib-dir /tmp/bioc-skill-lib --install-missing --out fgsea_summary.json.results for pathway, NES, padj, and leadingEdge.--describe-toy returns the expected toy gene and pathway counts.fgsea: rerun with --install-missing --lib-dir <path>.--min-size or inspect the ranked-statistics directionality.--seed.Rscript skills/systems-biology/fgsea-preranked-enrichment/scripts/run_fgsea_preranked.R --describe-toyreactome-identifiers-enrichmentclusterprofiler-custom-enrichment