Individual skill

integrative-analysis

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal correlation, chromatin state segmentation, enhancer-gene linkage, or any analysis that requires merging or comparing data from two or more ENCODE experiments. Covers same-assay cross-sample, multi-omic same-sample, cross-organism, and perturbation integration designs. Guides compatibility checks, batch effect detection, normalization, integration strategy selection, and provenance documentation.

plugin/skills/integrative-analysis/SKILL.md

Source commit 36836c8725fd4d20d9c851ce314f5151aea5f57c

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Observed behavior

Network or broad shell

Last checked

Nov 6, 2026

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