القائمة
Use this skill to run a lightweight Scanpy QC pass on a toy count matrix with the repository-managed Scanpy environment.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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 | scanpy-qc-starter |
| description | Use this skill to run a lightweight Scanpy QC pass on a toy count matrix with the repository-managed Scanpy environment. |
Provide a reproducible starting point for Scanpy-based QC work with toy matrix inputs, AnnData export, and a small verification report.
.h5ad artifactslurm/envs/scanpyslurm/envs/scanpy/bin/pythonexamples/toy_counts.tsv.python3 skills/transcriptomics/scanpy-qc-starter/scripts/preflight_counts.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsv.slurm/envs/scanpy/bin/python skills/transcriptomics/scanpy-qc-starter/scripts/run_scanpy_qc.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsv --summary-out skills/transcriptomics/scanpy-qc-starter/assets/scanpy_qc_summary.json --h5ad-out scratch/scanpy/toy_counts_qc.h5ad.total_counts, n_genes_by_counts, and pct_counts_mt in the summary output..h5ad file.slurm/envs/scanpy and rerun with that interpreter.python3 .../preflight_counts.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsvslurm/envs/scanpy/bin/python .../run_scanpy_qc.py --input skills/transcriptomics/scanpy-qc-starter/examples/toy_counts.tsv --summary-out scratch/scanpy/summary.json --h5ad-out scratch/scanpy/toy_counts.h5adsnakemake-toy-workflow-starter