Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs normal comparison, developmental time course, constitutive vs variable regulation, or multi-tissue data availability mapping. Handles batch effect detection, biosample hierarchy, and comparison design.
How to install compare-biosamples?
ammawla/encode-toolkit/compare-biosamples
$npx -y skills add ammawla/encode-toolkit --skill compare-biosamplesInstalls into the current project.
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Run `npx skills use "https://github.com/ammawla/encode-toolkit" --skill "ammawla/encode-toolkit/compare-biosamples"` 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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