Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, or generate summary reports. Trigger on: batch analysis, multiple experiments, bulk processing, experiment comparison, batch QC, multi-sample, batch download, experiment table, summary report, collection analysis.
How to install batch-analysis?
ammawla/encode-toolkit/batch-analysis
$npx -y skills add ammawla/encode-toolkit --skill batch-analysisInstalls into the current project.
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Run `npx skills use "https://github.com/ammawla/encode-toolkit" --skill "ammawla/encode-toolkit/batch-analysis"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/ammawla/encode-toolkit" that are relevant to the current task. Run `npx skills add "https://github.com/ammawla/encode-toolkit"` and select the relevant skills, then follow their instructions.
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