Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Stage 1 of the spatial transcriptomics workflow — load 10x Visium data and QC-filter low-quality spots.
Install Spatial S1 Load Qc
$ npx skills add QING1105/ezST --skill spatial-s1-load-qc -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install QING1105/ezST spatial-s1-load-qc --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s1-load-qc .claude/skills/spatial-s1-load-qc && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "spatial-s1-load-qc" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s1-load-qc into .claude/skills/spatial-s1-load-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s1-load-qc", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s1-load-qcType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add QING1105/ezST --skill spatial-s1-load-qc -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install QING1105/ezST spatial-s1-load-qc --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .agents/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s1-load-qc .agents/skills/spatial-s1-load-qc && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "spatial-s1-load-qc" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s1-load-qc into .agents/skills/spatial-s1-load-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s1-load-qc", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add QING1105/ezST --skill spatial-s1-load-qc -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install QING1105/ezST spatial-s1-load-qc --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s1-load-qc .cursor/skills/spatial-s1-load-qc && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "spatial-s1-load-qc" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s1-load-qc into .cursor/skills/spatial-s1-load-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s1-load-qc", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/QING1105/ezST.git --path plugins/spatial-transcriptomics/skills/s1-load-qc--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add QING1105/ezST --skill spatial-s1-load-qc -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install QING1105/ezST spatial-s1-load-qc --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s1-load-qc .gemini/skills/spatial-s1-load-qc && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "spatial-s1-load-qc" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s1-load-qc into .gemini/skills/spatial-s1-load-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s1-load-qc", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install QING1105/ezST spatial-s1-load-qcInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add QING1105/ezST --skill spatial-s1-load-qc -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .github/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s1-load-qc .github/skills/spatial-s1-load-qc && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "spatial-s1-load-qc" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s1-load-qc into .github/skills/spatial-s1-load-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s1-load-qc", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add QING1105/ezST --skill spatial-s1-load-qc -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install QING1105/ezST spatial-s1-load-qc --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/s1-load-qc .opencode/skills/spatial-s1-load-qc && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "spatial-s1-load-qc" agent skill from https://github.com/QING1105/ezST/tree/master/plugins/spatial-transcriptomics/skills/s1-load-qc into .opencode/skills/spatial-s1-load-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spatial-s1-load-qc", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
spatial-s1-load-qc- GitHub stars
- 101
- Token cost
- ~467 tokens
- SKILL.md length
- 154 words
- Files
- 1
- Skills in repo
- 11
- Repo updated
- First seen
- Licence
- MIT
At a glance
Stage 1 of the spatial transcriptomics workflow — load 10x Visium data and QC-filter low-quality spots.
- Works in 3 steps: Init project:… → Load data:… → Filter spots:…
- The user asks to load Visium data
- SKILL.md covers Goal, Steps, Outputs and Biological Interpretation, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Spatial S1 Load Qc is an agent skill from QING1105/ezST. 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.
Its SKILL.md is about 470 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics. It works with AnnData. The repository describes itself as: 10x Visium spatial transcriptomics analysis skills for Codex — staged workflow with human review gates and LLM biological interpretation. The licence is MIT.
When your agent uses it
- The user asks to load Visium data
- Initialize a spatial project
- Filter spots by quality (counts
- Mitochondrial fraction)
Example prompts
- “/spatial-s1-load-qc”
Workflow steps
3 steps, taken from the first numbered list in SKILL.md.
- Init project: init_spatial_project(project_dir=...) — creates the standardized directory layout.
- Load data: load_visium_data(counts_file=..., coordinates_file=..., sample_id=..., output_path=...)
- Filter spots: filter_visium_spots(adata_path=..., output_path=..., plot_path=..., min_counts=..., min_genes=..., pct_mt=...)
What it can do on your machine
Read from SKILL.md and the folder at commit 429f9fc. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Spatial S1 Load Qc loads about 467 tokens when it runs. Until then it costs about 82 tokens; SKILL.md has 154 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from QING1105/ezST at commit 429f9fc, republished under its MIT licence (© QING1105). 154 words, ~467 tokens.
Download SKILL.mdSave it as
.claude/skills/spatial-s1-load-qc/SKILL.md (or your agent's skills folder).- name
- spatial-s1-load-qc
- description
- 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.
- license
- MIT
S1 — Load + QC
Goal
Initialize the project, load Visium data into a standardized AnnData, and filter low-quality spots.
Steps
- Init project:
init_spatial_project(project_dir=...)— creates the standardized directory layout. - Load data:
load_visium_data(counts_file=..., coordinates_file=..., sample_id=..., output_path=...)- h5ad: pass the h5ad path as
counts_file(coordinates already embedded). - 10x matrix: pass matrix/barcodes/features paths.
- wide CSV: pass counts CSV + spot coordinates CSV.
- Output: h5ad with
X= raw counts,obsm['spatial'],obs['barcode'].
- h5ad: pass the h5ad path as
- Filter spots:
filter_visium_spots(adata_path=..., output_path=..., plot_path=..., min_counts=..., min_genes=..., pct_mt=...)- Defaults:
min_counts=500,min_genes=250,pct_mt=20(adjust if user specifies). - Output: filtered h5ad + QC violin/spatial plots.
- Defaults:
Outputs
results/01_loading/<sample>_loaded.h5adresults/02_qc/<sample>_filtered.h5adresults/02_qc/<sample>_qc_*.png(pre/post filter plots)
Biological Interpretation
- Report spots retained:
filtered n / raw nand the fraction removed. - Look at spatial plots: is the removed area consistent with tissue edges / low-quality regions?
- State whether thresholds were reasonable or should be tightened/loosened.
Stop for Review
Present interpretation using the template from the parent spatial-transcriptomics skill. Wait for 通过 / 调整 / 跳过 before proceeding to S2.
© QING1105, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in plugins/spatial-transcriptomics/skills/s1-load-qc of QING1105/ezST.
Open the folder on GitHubat commit 429f9fc
Compare with similar skills
Spatial S1 Load Qc next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Spatial S1 Load Qc this skillQING1105/ezST | 101 | — | ~467 | Automated safety check: Pass | MIT | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 33k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| ScgptJimLiu/science-skills | 228 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 33k | 11 repos | ~4k | Automated safety check: Pass | MIT | |
| Anndatadavila7/claude-code-templates | 33k | 11 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Single-Cell Initial AnalysisLigphiDonk/Oh-my--paper | 739 | 1 repos | ~1.4k | Automated safety check: Pass | MIT |
Similar skills
Scgpt
JimLiu/science-skills
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology.
PyDESeq2 Differential Expression
davila7/claude-code-templates
Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
Anndata
davila7/claude-code-templates
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling…
Single-Cell Initial Analysis
LigphiDonk/Oh-my--paper
Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.
Single Cell Data Prep Qc
harrisongzhang/TheVirtualBiotech
Single-cell RNA-seq data preparation and quality control pipeline.
More from QING1105/ezST
All 11 skills in this repoSpatial Transcriptomics
QING1105/ezST
End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
Spatial Visium Hd
QING1105/ezST
Visium HD platform branch of the spatial transcriptomics workflow — reconstruct single cells from 2 μm bins via morphological segmentation and bin-to-cell aggregation.
Spatial Atera
QING1105/ezST
Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis.
Spatial S3 Domains SVG
QING1105/ezST
Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes.
Spatial S4 Deconvolve
QING1105/ezST
Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.
Spatial S5 Downstream
QING1105/ezST
Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.
Related
Works with
Categories
Questions about Spatial S1 Load Qc
What does Spatial S1 Load Qc do?
Stage 1 of the spatial transcriptomics workflow — load 10x Visium data and QC-filter low-quality spots. Spatial S1 Load Qc is an agent skill from QING1105/ezST. Stage 1 of the spatial transcriptomics workflow — load 10x Visium data and QC-filter low-quality spots.
When should I use Spatial S1 Load Qc?
Spatial S1 Load Qc fits situations like: the user asks to load Visium data; initialize a spatial project; filter spots by quality (counts; mitochondrial fraction).
How do I install Spatial S1 Load Qc in Claude Code?
Run `npx skills add QING1105/ezST --skill spatial-s1-load-qc -a claude-code`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/s1-load-qc in QING1105/ezST) into .claude/skills/spatial-s1-load-qc in your project. Claude Code loads it when a task matches its description.
How do I install Spatial S1 Load Qc in Codex?
Run `npx skills add QING1105/ezST --skill spatial-s1-load-qc -a codex`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/s1-load-qc in QING1105/ezST) into .agents/skills/spatial-s1-load-qc in your project. Codex loads it when a task matches its description.
Can I use Spatial S1 Load Qc in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add QING1105/ezST --skill spatial-s1-load-qc -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/spatial-s1-load-qc, .gemini/skills/spatial-s1-load-qc, .github/skills/spatial-s1-load-qc and .opencode/skills/spatial-s1-load-qc in your project.
What does Spatial S1 Load Qc need to run?
SKILL.md names no scripts, command-line tools or credentials: Spatial S1 Load Qc is instructions for the agent only.
Does Spatial S1 Load Qc access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Spatial S1 Load Qc safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Spatial S1 Load Qc use?
Spatial S1 Load Qc is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Spatial S1 Load Qc use?
About 467 tokens (SKILL.md is roughly 1.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Spatial S1 Load Qc?
Skills that share tags, products or a category with Spatial S1 Load Qc: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars), Scgpt (JimLiu/science-skills, 228 stars), PyDESeq2 Differential Expression (davila7/claude-code-templates, 33k stars) and Anndata (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spatial S1 Load Qc?
QING1105 (a GitHub user) maintains it in QING1105/ezST, which has 101 GitHub stars. The repository holds 11 skills in this directory. The repository was last updated on August 26, 2026.
Source: QING1105/ezST on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.