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bio-spatial-transcriptomics-spatial-data-io

85 / 100 · Low risk

Fine to try.

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

Loads spatial transcriptomics data from Visium, Visium HD, Xenium, MERFISH/MERSCOPE, CosMx, Slide-seq/Curio, and Stereo-seq into AnnData or SpatialData using spatialdata-io and Squidpy. Use when deciding which platform class is in hand (imaging/in-situ vs sequencing/capture), which reader matches the platform (spatialdata_io.xenium/merscope/cosmx vs squidpy.read.visium/vizgen/nanostring), whether to work from the per-transcript molecule table (the re-segmentable source of truth) or the segmenta…

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