Agent skill

Sc Count

Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData.

MITAuto-check passedResearch & Science

Install Sc Count

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill sc-count -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw sc-count --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/singlecell/scrna/sc-count .claude/skills/sc-count && rm -rf skills-src

Use ~/.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/

Paste into Claude Code

Install the "sc-count" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-count into .claude/skills/sc-count/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-count", 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

$skill-installer install https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-count

Type 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.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill sc-count -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw sc-count --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/singlecell/scrna/sc-count .agents/skills/sc-count && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "sc-count" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-count into .agents/skills/sc-count/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-count", 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.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill sc-count -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw sc-count --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/singlecell/scrna/sc-count .cursor/skills/sc-count && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "sc-count" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-count into .cursor/skills/sc-count/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-count", 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

$ gemini skills install https://github.com/TianGzlab/OmicsClaw.git --path skills/singlecell/scrna/sc-count

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill sc-count -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw sc-count --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/singlecell/scrna/sc-count .gemini/skills/sc-count && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "sc-count" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-count into .gemini/skills/sc-count/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-count", 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.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw sc-count

Installs 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).

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill sc-count -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/singlecell/scrna/sc-count .github/skills/sc-count && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "sc-count" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-count into .github/skills/sc-count/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-count", 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.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill sc-count -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw sc-count --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/singlecell/scrna/sc-count .opencode/skills/sc-count && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "sc-count" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/scrna/sc-count into .opencode/skills/sc-count/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sc-count", 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: sc-count
GitHub stars: 161
Token cost: ~1.3k tokens
SKILL.md length: 390 words
Files: 8 (incl. references)
Skills in repo: 95
Repo updated: Jul 28, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData.

Works in 6 steps: Resolve --input; if it's an existing… → Otherwise validate backend prerequisites… → Run the chosen backend against the FASTQ… → …
Tasks that involve Bioinformatics
SKILL.md covers When to use, Inputs & Outputs, Flow and Gotchas, plus 2 more sections
Runs Python scripts from its folder; calls python

What it does

Sc Count is an agent skill from TianGzlab/OmicsClaw. Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData. Skip when reads are already counted into AnnData (use sc-standardize-input); raw quality assessment only (use sc-fastq-qc).

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including reference files (for example `references/methodology.md`, `references/output_contract.md` and `references/parameters.md`).

It sits in Research & Science, covering Bioinformatics. It works with AnnData and Python. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is MIT.

When your agent uses it

Tasks that involve Bioinformatics

Example prompts

“/sc-count”

Requirements

Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

Resolve --input; if it's an existing CellRanger / STARsolo / SimpleAF / kb-python output dir, re-canonicalise instead of running the…
Otherwise validate backend prerequisites (chemistry, reference, t2g for kb-python, whitelist for STARsolo).
Run the chosen backend against the FASTQ (and --read2 if explicit).
Load the resulting matrix into AnnData; canonicalise (layers["counts"], adata.raw, gene-name harmonisation).
Render barcode-rank + count-distribution figures.
Emit processed.h5ad + report.md + result.json.

What it can do on your machine

Read from SKILL.md and the folder at commit 6fbd79f. 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
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
- python
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

Sc Count loads about 1.3k tokens when it runs, and up to ~5.2k if it reads all its reference files. Until then it costs about 64 tokens; SKILL.md has 390 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~64
When it runs · the whole SKILL.md, loaded when a task matches: ~1.3k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~5.2k

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 TianGzlab/OmicsClaw at commit 6fbd79f, republished under its MIT licence (© TianGzlab). 390 words, ~1,329 tokens.

Download SKILL.mdSave it as .claude/skills/sc-count/SKILL.md (or your agent's skills folder). This skill also uses 7 other files; get the full folder from GitHub.

name: sc-count
description: Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData. Skip when reads are already counted into AnnData (use sc-standardize-input); raw quality assessment only (use sc-fastq-qc).
version: 0.3.0
author: OmicsClaw
license: MIT
emoji: 🧬
tags: singlecell, scrna, counting, cellranger, starsolo, simpleaf, kb-python
requires: anndata, matplotlib, numpy, pandas, scanpy, scipy, seaborn

sc-count

When to use

The user has FASTQ files (or pre-existing tool output directories) and wants per-cell counts in OmicsClaw's canonical AnnData contract. Four backends share one CLI: cellranger, starsolo, simpleaf, kb-python. When passed an already-counted directory the skill re-canonicalises rather than re-counts. Pairs with sc-fastq-qc upstream (read QC) and sc-multi-count downstream (merging multiple samples).

Inputs & Outputs

<!-- AUTO-GENERATED from skill.yaml (interface) — do not edit by hand. Regenerate: python scripts/generate_skill_md.py <skill_dir> -->

Inputs

Input kinds: file, directory
Modalities: scrna
File types: .fastq, .fq, .h5ad
FASTQ structure: valid first record; paired layout
Directory layouts (any): paired-fastq, tenx-matrix, cellranger-output, starsolo-output, pseudoalign-output

Outputs

tables/Summary.csv
tables/backend_summary.csv
tables/barcode_metrics.csv
tables/barcodes.tsv
tables/cell_metadata.csv
tables/count_summary.csv
tables/features.tsv
tables/genes.tsv
tables/metrics_summary.csv
tables/simpleaf_t2g.tsv
figures/barcode_rank.png
figures/count_complexity_scatter.png
figures/count_distributions.png
3M-february-2018.txt
737K-august-2016.txt
Aligned.sortedByCoord.out.bam
analysis_summary.txt
cells_x_genes.barcodes.txt
cells_x_genes.genes.txt
multiqc_report.html
possorted_genome_bam.bam
processed.h5ad
quants_mat_cols.txt
quants_mat_rows.txt
simpleaf_index.json
standardized_input.h5ad
web_summary.html
report.md
result.json
Processed AnnData (saves_h5ad)

Flow

Resolve --input; if it's an existing CellRanger / STARsolo / SimpleAF / kb-python output dir, re-canonicalise instead of running the backend.
Otherwise validate backend prerequisites (chemistry, reference, t2g for kb-python, whitelist for STARsolo).
Run the chosen backend against the FASTQ (and --read2 if explicit).
Load the resulting matrix into AnnData; canonicalise (layers["counts"], adata.raw, gene-name harmonisation).
Render barcode-rank + count-distribution figures.
Emit processed.h5ad + report.md + result.json.

Show full SKILL.md (206 more words)Show less

Gotchas

Missing input path → hard fail. sc_count.py:356 raises FileNotFoundError(f"Input path not found: {input_path}"). Common when the FASTQ dir is on a network mount that has not been resolved at run time.
STARsolo requires explicit chemistry. sc_count.py:420 raises ValueError("STARsolo runs require an explicit --chemistryvalue such as10xv3.") when chemistry is left at the auto default. STARsolo currently supports 10xv2, 10xv3, and 10xv4; pass one of those.
Backend prerequisites are validated up front. sc_count.py:401, :423, :451 raise ValueError for missing --reference (CellRanger/STARsolo/simpleaf), missing --t2g (kb-python), or unsupported --chemistry for STARsolo. No silent fallback to a different backend — pick a feasible one before invoking.
Re-canonicalising-existing-output is detected by directory shape, not a flag. If --input points at a CellRanger output dir (e.g. one with outs/raw_feature_bc_matrix/), the skill skips counting and just imports the matrix. No flag separates the two paths; verify by inspecting result.json["data"]["execution"] (empty list = re-canonicalise; populated = backend invoked) or by reading tables/backend_summary.csv (lists the backend metrics only when the backend ran).

Key CLI

bash

# Demo (synthetic FASTQ + CellRanger-shaped output)
python omicsclaw.py run sc-count --demo --output /tmp/sc_count_demo

# CellRanger over FASTQ
python omicsclaw.py run sc-count \
  --input fastq_dir/ --output results/ \
  --reference cellranger_transcriptome --threads 16

# STARsolo (requires explicit chemistry)
python omicsclaw.py run sc-count \
  --input fastq_dir/ --output results/ \
  --reference star_genome_dir --chemistry 10xv3 --whitelist barcodes.tsv

# Re-canonicalise an existing CellRanger output directory
python omicsclaw.py run sc-count \
  --input cellranger_output_dir/ --output results/

Files

SKILL.md and 7 other files (references) in skills/singlecell/scrna/sc-count of TianGzlab/OmicsClaw.

SKILL.md
references/methodology.md
references/output_contract.md
references/parameters.md
references/r_visualization.md
sc_count.py
skill.yaml
tests/test_sc_count.py

Open the folder on GitHubat commit 6fbd79f

Compare with similar skills

Sc Count 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.

Sc Count compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Sc Count this skillTianGzlab/OmicsClaw	161	—	~1.3k	Automated safety check: Pass	MIT	2 mo ago
PyDESeq2 Differential Expressiondavila7/claude-code-templates	32k	12 repos	~4k	Automated safety check: Pass	MIT	today
Anndatadavila7/claude-code-templates	32k	12 repos	~2.5k	Automated safety check: Pass	MIT	today
GenimlK-Dense-AI/scientific-agent-skills	48k	2 repos	~4k	Automated safety check: Notes	MIT	2 days ago
ScanpyK-Dense-AI/scientific-agent-skills	48k	1 repos	~5.1k	Automated safety check: Pass	BSD-3-Clause	2 days ago
AnndataK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.9k	Automated safety check: Notes	BSD-3-Clause	2 days ago

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Questions about Sc Count

What does Sc Count do?

Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData. Sc Count is an agent skill from TianGzlab/OmicsClaw. Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData.

When should I use Sc Count?

Sc Count fits situations like: tasks that involve Bioinformatics.

How do I install Sc Count in Claude Code?

Run `npx skills add TianGzlab/OmicsClaw --skill sc-count -a claude-code`. Or copy the skill folder (skills/singlecell/scrna/sc-count in TianGzlab/OmicsClaw) into .claude/skills/sc-count in your project. Claude Code loads it when a task matches its description.

How do I install Sc Count in Codex?

Run `npx skills add TianGzlab/OmicsClaw --skill sc-count -a codex`. Or copy the skill folder (skills/singlecell/scrna/sc-count in TianGzlab/OmicsClaw) into .agents/skills/sc-count in your project. Codex loads it when a task matches its description.

Can I use Sc Count 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 TianGzlab/OmicsClaw --skill sc-count -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/sc-count, .gemini/skills/sc-count, .github/skills/sc-count and .opencode/skills/sc-count in your project.

What does Sc Count need to run?

Going by SKILL.md and its folder, Sc Count needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Sc Count 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 Sc Count 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 Sc Count use?

Sc Count 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 Sc Count use?

About 1.3k tokens (SKILL.md is roughly 5.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 3.9k tokens, read only when the agent opens those files.

What are the alternatives to Sc Count?

Skills that share tags, products or a category with Sc Count: PyDESeq2 Differential Expression (davila7/claude-code-templates, 32k stars), Anndata (davila7/claude-code-templates, 32k stars), Geniml (K-Dense-AI/scientific-agent-skills, 48k stars) and Scanpy (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Sc Count?

TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 95 skills in this directory. The repository was last updated on July 28, 2026.

Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Sc Count

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

sc-count

When to use

Inputs & Outputs

Flow

Gotchas

Key CLI

See also

Files

Compare with similar skills

Similar skills

More from TianGzlab/OmicsClaw

Related

Questions about Sc Count