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bio-single-cell-hashing-demultiplexing

85 / 100 · Low risk

Fine to try.

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

Assign cells to their sample of origin from cell or nucleus hashing (CITE-seq HTOs, MULTI-seq lipid/cholesterol tags, CellPlex CMOs) and call cross-sample doublets using Seurat HTODemux/MULTIseqDemux, hashsolo, demuxEM, GMM-Demux, and demuxmix. Use when assigning pooled hashed cells back to their sample, calling cross-sample doublets from HTO counts, choosing a demultiplexing method, deciding between hashtag and genetic demultiplexing, or rescuing an oversized Negative pile from weak HTO staini…

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-single-cell-hashing-demultiplexing' ] || [ -L ~/.agents/skills/'bio-single-cell-hashing-demultiplexing' ]; then echo 'A skill folder named bio-single-cell-hashing-demultiplexing 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-single-cell-hashing-demultiplexing' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-single-cell-hashing-demultiplexing' ~/.agents/skills/'bio-single-cell-hashing-demultiplexing' && 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-single-cell-hashing-demultiplexing' ~/.claude/skills/'bio-single-cell-hashing-demultiplexing' (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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