Individual skill

single-cell-encode

Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs bulk profiles. Covers platform differences (10X Chromium, Smart-seq2, Drop-seq), quality limitations of single-cell data, multimodal integration (RNA+ATAC), and cross-study reproducibility concerns. Also use for cell type annotation, gene detection limits, dropout artifacts, and single-cell data structure in ENCODE.

plugin/skills/single-cell-encode/SKILL.md

Source commit 36836c8725fd4d20d9c851ce314f5151aea5f57c

What was checked

Matches the observed repository HEAD

Yes

Scanner rules are current

Yes

Repository scan complete

No

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No

Observed behavior

Network or broad shell

Last checked

Nov 6, 2026

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