Agent skill

Bulkrna Deconvolution

Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Deconvolution

skills CLI

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

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

GitHub CLI

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

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-deconvolution -a codex

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

GitHub CLI

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

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

GitHub CLI

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

--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-deconvolution -a gemini-cli

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

GitHub CLI

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

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-deconvolution -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-deconvolution .github/skills/bulkrna-deconvolution && 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-deconvolution" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-deconvolution into .github/skills/bulkrna-deconvolution/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-deconvolution", 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-deconvolution -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-deconvolution --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-deconvolution .opencode/skills/bulkrna-deconvolution && 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-deconvolution" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-deconvolution into .opencode/skills/bulkrna-deconvolution/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-deconvolution", 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-deconvolution
GitHub stars: 161
Token cost: ~757 tokens
SKILL.md length: 207 words
Files: 10 (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 estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.

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 Deconvolution is an agent skill from TianGzlab/OmicsClaw. Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference. Skip when the data is already single-cell (no deconvolution needed); spatial deconvolution (use spatial-deconv).

Its SKILL.md is about 760 tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including reference files (for example `_api.py`, `bulkrna_deconvolution.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-deconvolution”

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 Deconvolution loads about 757 tokens when it runs, and up to ~1.8k if it reads all its reference files. Until then it costs about 63 tokens; SKILL.md has 207 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~63
When it runs · the whole SKILL.md, loaded when a task matches: ~757
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.8k

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). 207 words, ~757 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-deconvolution/SKILL.md (or your agent's skills folder). This skill also uses 9 other files; get the full folder from GitHub.

name: bulkrna-deconvolution
description: Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference. Skip when the data is already single-cell (no deconvolution needed); spatial deconvolution (use spatial-deconv).
trigger: bulk deconvolution, cell type proportion, NNLS, CIBERSORTx, bulk deconv, cell fraction
tags: bulkrna, deconvolution, NNLS, cell-type-proportion

bulkrna-deconvolution

When to use

Estimate bulk cell-type proportions with an explicit signature matrix. 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-deconvolution")
# Supply DataFrames read with read_input(..., reader=...) for your CSV layout.
result = library.deconvolve(counts, signature=signature)
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 -->

`deconvolve(counts, *, signature)`

Estimate sample proportions without changing either input.

:param counts: Nonnegative gene-by-sample expression DataFrame. :param signature: Required gene-by-cell-type reference, matching the CLI --reference. :returns: Sample-by-cell-type DataFrame; diagnostics contain residuals and shared genes. :raises ValueError: Matrices have invalid values, duplicate labels or no shared genes.

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

Read reference overlap and reconstruction diagnostics.

:param result: DataFrame returned by deconvolve. :param keep: Default True; False removes diagnostics from attrs. :returns: Diagnostic dictionary, empty after removal.

`proportions_figure(result)`

Plot estimated cell-type proportions per sample.

:param result: Sample-by-cell-type DataFrame from deconvolve. :returns: A matplotlib Figure, without writing files. :raises ValueError: The table cannot be plotted as numeric proportions.

<!-- api:end -->

Methods and parameters

See parameters and methodology.

Gotchas

deconvolve requires shared gene identifiers and nonnegative matrices.
run_info()['residuals'] measures fit to the supplied reference, not confidence intervals.
NNLS is the only backend; deconvolve does not call CIBERSORTx or MuSiC.

Inputs and outputs

The library returns objects without file writes. CLI inventory:

Inputs

File types: .csv

Outputs

tables/dominant_types.csv
tables/proportions.csv
figures/mean_proportions_pie.png
figures/proportions_heatmap.png
figures/proportions_stacked.png
report.md
result.json

CLI

bash

python skills/bulkrna/bulkrna-deconvolution/bulkrna_deconvolution.py --demo --output /tmp/bulkrna-deconvolution

Dependencies

matplotlib, numpy, pandas, scipy

Files

SKILL.md and 9 other files (references) in skills/bulkrna/bulkrna-deconvolution of TianGzlab/OmicsClaw.

SKILL.md
_api.py
bulkrna_deconvolution.py
examples/example_step.py
references/methodology.md
references/output_contract.md
references/parameters.md
tests/__init__.py
tests/test_api.py
tests/test_bulkrna_deconvolution.py

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Bulkrna Deconvolution 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 Deconvolution compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Bulkrna Deconvolution this skillTianGzlab/OmicsClaw	161	—	~757	Automated safety check: Pass	Apache-2.0	today
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	3 repos	~3.4k	Automated safety check: Notes	Apache-2.0	23 days ago
Metabolic Study Planneraiming-lab/AutoResearchClaw	15k	—	~1.9k	Automated safety check: Pass	MIT	1 mo ago
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.2k	Automated safety check: Pass	MIT	3 days ago
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	23 days ago
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw	15k	—	~923	Automated safety check: Pass	MIT	1 mo ago

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Questions about Bulkrna Deconvolution

What does Bulkrna Deconvolution do?

Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference. Bulkrna Deconvolution is an agent skill from TianGzlab/OmicsClaw. Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.

When should I use Bulkrna Deconvolution?

Bulkrna Deconvolution fits situations like: tasks that involve Bioinformatics.

How do I install Bulkrna Deconvolution in Claude Code?

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

How do I install Bulkrna Deconvolution in Codex?

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

Can I use Bulkrna Deconvolution 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-deconvolution -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-deconvolution, .gemini/skills/bulkrna-deconvolution, .github/skills/bulkrna-deconvolution and .opencode/skills/bulkrna-deconvolution in your project.

What does Bulkrna Deconvolution need to run?

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

Does Bulkrna Deconvolution 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 Deconvolution 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 Deconvolution use?

Bulkrna Deconvolution 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 Deconvolution use?

About 757 tokens (SKILL.md is roughly 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 1k tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Deconvolution?

Skills that share tags, products or a category with Bulkrna Deconvolution: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bulkrna Deconvolution?

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 Deconvolution

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-deconvolution

When to use

Use from a step

API

deconvolve(counts, *, signature)

run_info(result, *, keep=True)

proportions_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 Deconvolution

`deconvolve(counts, *, signature)`

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

`proportions_figure(result)`