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bio-spatial-transcriptomics-spatial-deconvolution

85 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Estimates per-spot cell type composition of spatial transcriptomics mixtures (Visium, Slide-seq, Stereo-seq) from an scRNA-seq reference with cell2location, RCTD, SPOTlight, stereoscope, SpatialDWLS, or reference-free STdeconvolve. Use when deciding whether a platform even needs deconvolution (the resolution fork -- a 55um Visium spot is a 1-10-cell MIXTURE -> deconvolve, but a Xenium/MERFISH/CosMx cell is already single -> segment instead, and running deconvolution there invents fractions that…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-spatial-transcriptomics-spatial-deconvolution' ] || [ -L ~/.agents/skills/'bio-spatial-transcriptomics-spatial-deconvolution' ]; then echo 'A skill folder named bio-spatial-transcriptomics-spatial-deconvolution already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-spatial-transcriptomics-spatial-deconvolution' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-spatial-transcriptomics-spatial-deconvolution' ~/.agents/skills/'bio-spatial-transcriptomics-spatial-deconvolution' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-spatial-transcriptomics-spatial-deconvolution' ~/.claude/skills/'bio-spatial-transcriptomics-spatial-deconvolution' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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