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spatial-mapping-tangram

95 / 100 · Low risk

Fine to try. Some of what it can do is expected: a coding skill usually runs build and test commands.

By jaechang-hits/SciAgent-Skills (GitHub) · coding · 388 stars · scanned at commit 65d6ceb

Tangram (tangram-sc) mapping of scRNA-seq onto spatial transcriptomics (Visium, Slide-seq, MERFISH, Xenium), one skill for every Tangram task: marker training genes, cells/clusters/constrained mode, per-spot cell type proportions, held-out gene validation (training scores, compare_spatial_geneexp, AUC, k-fold CV), imputation of unmeasured or dropout genes (project_genes; gimVI alternative), and Visium deconvolution into segmented nuclei with the tissue image (squidpy watershed, target_count, de…

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/'spatial-mapping-tangram' ] || [ -L ~/.agents/skills/'spatial-mapping-tangram' ]; then echo 'A skill folder named spatial-mapping-tangram already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/jaechang-hits/SciAgent-Skills' "$d" && git -C "$d" checkout --quiet '65d6ceb875e20b751ffb3a6d8ee19516558789e1' -- 'skills/genomics-bioinformatics/spatial-transcriptomics/spatial-mapping-tangram' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/genomics-bioinformatics/spatial-transcriptomics/spatial-mapping-tangram' ~/.agents/skills/'spatial-mapping-tangram' && 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/'spatial-mapping-tangram' ~/.claude/skills/'spatial-mapping-tangram' (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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