Updated 1w ago
by QING1105
ezST
10x Visium spatial transcriptomics analysis skills for Codex — staged workflow with human review gates and LLM biological interpretation.
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- 11 skills (11 skills found in its SKILL.md files)
- 1 forks (1 forks)
- 1w ago last update (Last updated 1w ago)
Install
Skills CLI
npx skills add QING1105/ezST
Asks which skills and agents to install. Just one: npx skills add QING1105/ezST --skill spatial-s1-load-qc — add -g for every project.
Claude Code
git clone https://github.com/QING1105/ezSTcp -r "ezST/plugins/spatial-transcriptomics/skills/s1-load-qc" ~/.claude/skills/
Copies the spatial-s1-load-qc skill into ~/.claude/skills/ for every project (use .claude/skills/ for one project). Repeat for the other skills listed below.
Plugin
/plugin marketplace add QING1105/ezST
Run inside Claude Code if the repository ships a plugin marketplace, then pick plugins from /plugin.
Skills can run code on your machine — read the SKILL.md first.
What it does
In the author's own words, from each skill's SKILL.md.
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spatial-s1-load-qc
Stage 1 of the spatial transcriptomics workflow — load 10x Visium data and QC-filter low-quality spots. Use when the user asks to load Visium data, initialize a spatial project, or filter spots by quality (counts, genes, mitochondrial fraction). Produces QC plots and a filtered AnnData, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ s1-load-qc/ SKILL.md -
spatial-s2-normalize-cluster
Stage 2 of the spatial transcriptomics workflow — normalize 10x Visium data and cluster spatial spots. Use when the user asks to normalize, log-transform, find highly variable genes, or cluster Visium spots (PCA/UMAP/Leiden). Produces UMAP and spatial cluster plots, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ s2-normalize-cluster/ SKILL.md -
spatial-s3-domains-svg
Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes. Use when the user asks to find spatial domains/niches, run Moran's I, or detect spatially variable genes (SVGs) in Visium data. Produces spatial domain maps and SVG rankings, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ s3-domains-svg/ SKILL.md -
spatial-s4-deconvolve
Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions. Use when the user asks to deconvolve spatial spots, estimate cell-type composition, or run DestVI / SPOTlight with a scRNA-seq reference. Produces cell-type proportion maps, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ s4-deconvolve/ SKILL.md -
spatial-s5-downstream
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis. Use when the user asks to compute cell-type neighborhood enrichment (co-localization) or infer cell-cell communication with CellChat on Visium data. Produces enrichment heatmaps and CellChat network plots, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ s5-downstream/ SKILL.md -
spatial-atera
Analyze the user's 10x Atera cell-level data, loading native AnnData Zarr or h5ad, validating counts and segmentation, visualizing cell types in tissue space, and continuing through expression, spatial domains, neighborhood and communication analysis with review at each stage.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ spatial-atera/ SKILL.md -
spatial-downstream
Shared downstream analysis for all spatial platforms (Visium, Visium HD, Xenium, Atera) — neighborhood enrichment, CellChat cell-cell communication, and RNA velocity. Use after any platform branch has produced an h5ad with cell-type labels (classic Visium: deconvolution proportions; Visium HD / Xenium / Atera: cell-type annotations). Produces communication and trajectory results, then stops for r…
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ spatial-downstream/ SKILL.md -
spatial-transcriptomics
End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates. Use when the user asks to analyze Visium / spatial transcriptomics data, run spatial analysis pipelines (load, QC, normalize, cluster, spatial domains, SVG, deconvolution, neighborhood enrichment, cell-cell communication), or interpret spatial plots biologically. Each stage produces plots…
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ spatial-transcriptomics/ SKILL.md -
spatial-visium-hd
Visium HD platform branch of the spatial transcriptomics workflow — reconstruct single cells from 2 μm bins via morphological segmentation and bin-to-cell aggregation. Use when the user's data has binned_outputs/square_002um (Visium HD Space Ranger output). Produces a cell-level h5ad, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ spatial-visium-hd/ SKILL.md -
spatial-visium
Classic Visium platform branch of the spatial transcriptomics workflow — spot-level 5-stage pipeline (load+QC, normalize+cluster, domains+SVG, deconvolution, downstream prep). Use when the user's data is classic 10x Visium spot-level output (55 μm spots). Produces a spot-level h5ad + deconvolution results, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ spatial-visium/ SKILL.md -
spatial-xenium
Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis. Use when the user's data is 10x Xenium output (cell_feature_matrix.h5, cell-level h5ad, or transcripts.csv + segmentation). Produces a cell-level h5ad, then stops for review.
plugins/spatial-transcriptomics/ on GitHub (opens in a new tab)skills/ spatial-xenium/ SKILL.md
No skill matches that filter.
Review before you install
A skill is a set of instructions and scripts your agent will follow, and it can run code on your machine. Read the SKILL.md and any scripts first — this listing is not a security review.
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