Agent skill

Bulkrna Qc

Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Qc

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill bulkrna-qc -a claude-code

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

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw bulkrna-qc --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/bulkrna/bulkrna-qc .claude/skills/bulkrna-qc && 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 "bulkrna-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-qc into .claude/skills/bulkrna-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-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

$skill-installer install https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-qc

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 bulkrna-qc -a codex

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

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw bulkrna-qc --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/bulkrna/bulkrna-qc .agents/skills/bulkrna-qc && 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 "bulkrna-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-qc into .agents/skills/bulkrna-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-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.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill bulkrna-qc -a cursor

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

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw bulkrna-qc --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/bulkrna/bulkrna-qc .cursor/skills/bulkrna-qc && 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 "bulkrna-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-qc into .cursor/skills/bulkrna-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-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

$ gemini skills install https://github.com/TianGzlab/OmicsClaw.git --path skills/bulkrna/bulkrna-qc

--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 bulkrna-qc -a gemini-cli

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

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw bulkrna-qc --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/bulkrna/bulkrna-qc .gemini/skills/bulkrna-qc && 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 "bulkrna-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-qc into .gemini/skills/bulkrna-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-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.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw bulkrna-qc

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

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill bulkrna-qc -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 bulkrna-qc --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/bulkrna/bulkrna-qc .opencode/skills/bulkrna-qc && 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 "bulkrna-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-qc into .opencode/skills/bulkrna-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-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: bulkrna-qc
GitHub stars: 161
Token cost: ~789 tokens
SKILL.md length: 235 words
Files: 9 (incl. references)
Skills in repo: 88
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE.

Tasks that involve Bioinformatics
SKILL.md covers When to use, Use from a step, API and Methods and parameters, plus 5 more sections
Runs Python scripts from its folder; calls python

What it does

Bulkrna Qc is an agent skill from TianGzlab/OmicsClaw. Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE. Skip when data is raw FASTQ (use bulkrna-read-qc); aligner logs (use bulkrna-read-alignment); single-cell counts (use sc-qc).

Its SKILL.md is about 790 tokens, which your agent loads only when the skill is triggered. The skill folder holds 11 other files, including reference files (for example `_api.py`, `bulkrna_qc.py` and `examples/example_step.py`).

It sits in Research & Science, covering Bioinformatics. 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 Apache-2.0.

When your agent uses it

Tasks that involve Bioinformatics

Example prompts

“/bulkrna-qc”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 90a3bec. 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

Bulkrna Qc loads about 789 tokens when it runs, and up to ~1.9k if it reads all its reference files. Until then it costs about 68 tokens; SKILL.md has 235 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~68
When it runs · the whole SKILL.md, loaded when a task matches: ~789
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.9k

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 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 235 words, ~789 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-qc/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.

name: bulkrna-qc
description: Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE. Skip when data is raw FASTQ (use bulkrna-read-qc); aligner logs (use bulkrna-read-alignment); single-cell counts (use sc-qc).
trigger: bulk QC, library size, count matrix, sample quality, gene detection, RNA-seq quality, count QC
tags: bulkrna, QC, count-matrix, library-size, gene-detection, sample-correlation, CPM

bulkrna-qc

When to use

Assess raw integer count matrices before bulk differential expression. See the description for adjacent skills.

Use from a step

python

from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("bulkrna-qc")
# Supply DataFrames read with read_input(..., reader=...) for your CSV layout.
result = library.assess(counts)
write_output(result, "tables/result.csv")

The synthetic worked step is in examples/example_step.py.

API

<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->

`assess(counts)`

Measure library size and detection on raw counts without changing input.

:param counts: Gene-by-sample nonnegative integer DataFrame with unique labels. :returns: Sample-indexed DataFrame with QC metrics and diagnostic attrs. :raises ValueError: The matrix is invalid or a sample has no counts.

`run_info(result, *, keep=True)`

Read QC diagnostics and auxiliary matrices.

:param result: DataFrame returned by assess. :param keep: Default True; False removes diagnostics from result.attrs. :returns: A diagnostic dictionary, empty when no record remains.

`normalized_counts(result)`

Return CPM for visualization, not differential-expression input.

:param result: DataFrame returned by assess with its diagnostics retained. :returns: New gene-by-sample CPM DataFrame. :raises KeyError: QC diagnostics have been removed.

`library_figure(result)`

Plot total counts per sample without saving files.

:param result: QC table returned by assess. :returns: A matplotlib Figure; the caller saves and closes it. :raises KeyError: total_counts is missing.

<!-- api:end -->

Methods and parameters

See parameters and methodology.

Gotchas

assess rejects empty libraries instead of producing undefined CPM.
normalized_counts returns CPM for figures, not DE input.
run_info()['outlier_samples'] is correlation-based; check biological groups before removing samples.

Inputs and outputs

The library returns objects without file writes. CLI inventory:

Inputs

File types: .csv

Outputs

tables/cpm_normalized.csv
tables/sample_stats.csv
figures/expression_density.png
figures/gene_detection.png
figures/library_sizes.png
figures/sample_correlation.png
report.md
result.json

CLI

bash

python skills/bulkrna/bulkrna-qc/bulkrna_qc.py --demo --output /tmp/bulkrna-qc

Dependencies

matplotlib, numpy, pandas, scipy

Files

SKILL.md and 8 other files (references) in skills/bulkrna/bulkrna-qc of TianGzlab/OmicsClaw.

SKILL.md
_api.py
bulkrna_qc.py
examples/example_step.py
references/methodology.md
references/output_contract.md
references/parameters.md
tests/test_api.py
tests/test_interfaces.py

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Bulkrna 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.

Bulkrna Qc compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Bulkrna Qc this skillTianGzlab/OmicsClaw	161	—	~789	Automated safety check: Pass	Apache-2.0	2 days ago
Scanpy Single-Cell Analysisdavila7/claude-code-templates	33k	15 repos	~2.8k	Automated safety check: Pass	MIT	today
deepTools NGS Toolkitdavila7/claude-code-templates	33k	12 repos	~4.5k	Automated safety check: Pass	MIT	today
LaminDB Biological Data Managementdavila7/claude-code-templates	33k	12 repos	~3.6k	Automated safety check: Pass	MIT	today
PyDESeq2 Differential Expressiondavila7/claude-code-templates	33k	11 repos	~4k	Automated safety check: Pass	MIT	today
Gtars Genomic Interval Toolkitdavila7/claude-code-templates	33k	11 repos	~1.9k	Automated safety check: Pass	MIT	today

Similar skills

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.
33k GitHub starsUsed in 15 repos~2.8k tokens
Research & ScienceAuto-check passed
deepTools NGS Toolkit
davila7/claude-code-templates
Guides use of deepTools on sequencing data: BAM to bigWig conversion, QC, sample correlation, and heatmaps or profiles around TSS and peaks for ChIP-seq, RNA-seq and ATAC-seq.
33k GitHub starsUsed in 12 repos~4.5k tokens
Research & ScienceAuto-check passed
LaminDB Biological Data Management
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Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.
33k GitHub starsUsed in 12 repos~3.6k tokens
Research & ScienceAuto-check passed
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.
33k GitHub starsUsed in 11 repos~4k tokens
Research & ScienceAuto-check passed
Gtars Genomic Interval Toolkit
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Works with genomic intervals using gtars, a Rust toolkit with Python bindings: overlap detection, coverage tracks, tokenization for ML models and reference sequences.
33k GitHub starsUsed in 11 repos~1.9k tokens
Research & ScienceAuto-check passed
Single-Cell Initial Analysis
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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.
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Research & ScienceAuto-check passed

Questions about Bulkrna Qc

What does Bulkrna Qc do?

Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE. Bulkrna Qc is an agent skill from TianGzlab/OmicsClaw. Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE.

When should I use Bulkrna Qc?

Bulkrna Qc fits situations like: tasks that involve Bioinformatics.

How do I install Bulkrna Qc in Claude Code?

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

How do I install Bulkrna Qc in Codex?

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

Can I use Bulkrna 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 TianGzlab/OmicsClaw --skill bulkrna-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/bulkrna-qc, .gemini/skills/bulkrna-qc, .github/skills/bulkrna-qc and .opencode/skills/bulkrna-qc in your project.

What does Bulkrna Qc need to run?

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

Does Bulkrna 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 Bulkrna 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 Bulkrna Qc use?

Bulkrna Qc is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Bulkrna Qc use?

About 789 tokens (SKILL.md is roughly 3.2k 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 1.1k tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Qc?

Skills that share tags, products or a category with Bulkrna Qc: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars), deepTools NGS Toolkit (davila7/claude-code-templates, 33k stars), LaminDB Biological Data Management (davila7/claude-code-templates, 33k stars) and PyDESeq2 Differential Expression (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 Bulkrna Qc?

TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 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 Bulkrna Qc

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

bulkrna-qc

When to use

Use from a step

API

assess(counts)

run_info(result, *, keep=True)

normalized_counts(result)

library_figure(result)

Methods and parameters

Gotchas

Inputs and outputs

CLI

See also

Dependencies

Files

Compare with similar skills

Similar skills

More from TianGzlab/OmicsClaw

Related

Questions about Bulkrna Qc

`assess(counts)`

`run_info(result, *, keep=True)`

`normalized_counts(result)`

`library_figure(result)`