Agent skill

Bulkrna Cosinor Rhythm

Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Cosinor Rhythm

skills CLI

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

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

GitHub CLI

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

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-cosinor-rhythm -a codex

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

GitHub CLI

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

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

GitHub CLI

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

--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-cosinor-rhythm -a gemini-cli

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

GitHub CLI

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

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-cosinor-rhythm -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/run-derived/bulkrna-cosinor-rhythm .github/skills/bulkrna-cosinor-rhythm && 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-cosinor-rhythm" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/run-derived/bulkrna-cosinor-rhythm into .github/skills/bulkrna-cosinor-rhythm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-cosinor-rhythm", 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-cosinor-rhythm -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-cosinor-rhythm --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/run-derived/bulkrna-cosinor-rhythm .opencode/skills/bulkrna-cosinor-rhythm && 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-cosinor-rhythm" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/run-derived/bulkrna-cosinor-rhythm into .opencode/skills/bulkrna-cosinor-rhythm/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-cosinor-rhythm", 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-cosinor-rhythm
GitHub stars: 161
Token cost: ~840 tokens
SKILL.md length: 298 words
Files: 20 (incl. references)
Skills in repo: 88
Repo updated: Oct 7, 2026
First seen: Oct 8, 2026
Licence: Apache-2.0

At a glance

Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.

Works in 5 steps: Load --input or the repository-bound… → Parse time and replicate identities from… → Fit mesor + beta_cos*cos(2*pi*t/24) +… → …
Needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV
SKILL.md covers Purpose, Inputs & Outputs, API and Flow, plus 4 more sections
Runs Python scripts from its folder; calls python

What it does

Bulkrna Cosinor Rhythm is an agent skill from TianGzlab/OmicsClaw. Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV. Skip when an existing bulkrna skill already covers the request.

Its SKILL.md is about 840 tokens, which your agent loads only when the skill is triggered. The skill folder holds 22 other files, including reference files (for example `_api.py`, `bulkrna_cosinor_rhythm.py` and `completion_report.json`).

It sits in Research & Science, covering Bioinformatics and CSV and tabular files. 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

Needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV
Tasks that involve Bioinformatics
Tasks that involve CSV and tabular files

Example prompts

“/bulkrna-cosinor-rhythm”

Requirements

Python 3

Workflow steps

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

Load --input or the repository-bound demo dataset via --demo.
Parse time and replicate identities from the sample columns.
Fit mesor + beta_cos*cos(2*pi*t/24) + beta_sin*sin(2*pi*t/24) by OLS.
Derive amplitude, phase, fit statistics, and the per-gene rhythmicity verdict.
Write cosinor_results.csv, semantic_summary.json, report.md, and the standard result envelope.

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, from the files we listed), 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 Cosinor Rhythm loads about 840 tokens when it runs, and up to ~20k if it reads all its reference files. Until then it costs about 56 tokens; SKILL.md has 298 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~56
When it runs · the whole SKILL.md, loaded when a task matches: ~840
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~20k

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). 298 words, ~840 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-cosinor-rhythm/SKILL.md (or your agent's skills folder). This skill also uses 19 other files; get the full folder from GitHub.

name: bulkrna-cosinor-rhythm
description: Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV. Skip when an existing bulkrna skill already covers the request.
trigger: cosinor, circadian rhythmicity, 24-hour rhythm, bulk RNA time course
tags: bulkrna, autogenerated, skill-scaffold

bulkrna-cosinor-rhythm

Purpose

Use this Skill for a bulk RNA time-course CSV whose sample columns follow T{hour}_R{replicate} and require a deterministic 24-hour, single-component cosinor OLS fit per gene. Use another method when the period must be estimated, the design has covariates, or multi-harmonic/non-sinusoidal rhythms are needed.

Inputs & Outputs

Outputs

report.md
result.json
cosinor_results.csv
semantic_summary.json

API

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

`fit(timecourse)`

Fit a fixed 24-hour sinusoid independently to each gene.

:param timecourse: Gene-indexed DataFrame with T00_R1-style sample columns. :returns: Parameter DataFrame with descriptive rhythmic flags and diagnostics. :raises ValueError: Empty data, missing time columns or infinite expression.

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

Read gene counts and time-column filtering decisions.

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

`rhythm_figure(result)`

Plot fitted amplitude against phase, without writing files.

:param result: Parameter DataFrame returned by fit. :returns: matplotlib Figure. :raises KeyError: Parameter columns are missing.

<!-- api:end -->

Flow

Load --input <csv> or the repository-bound demo dataset via --demo.
Parse time and replicate identities from the sample columns.
Fit mesor + beta_cos*cos(2*pi*t/24) + beta_sin*sin(2*pi*t/24) by OLS.
Derive amplitude, phase, fit statistics, and the per-gene rhythmicity verdict.
Write cosinor_results.csv, semantic_summary.json, report.md, and the standard result envelope.

Gotchas

cosinor_results.csv marks rhythmic genes with descriptive thresholds (R-squared ≥ 0.8 and amplitude/mesor ≥ 0.2), not a significance test.
semantic_summary.json lists columns dropped for more than 20% missing values. Duplicate gene identifiers keep their first row; fits with insufficient observations or a singular design return missing parameters.
cosinor_results.csv uses a fixed 24-hour period; --method is retained as a report label, not a backend selector.

Key CLI

bash

# Demo
python skills/bulkrna/run-derived/bulkrna-cosinor-rhythm/bulkrna_cosinor_rhythm.py --demo --output /tmp/bulkrna-cosinor-rhythm_demo

# Real input
python skills/bulkrna/run-derived/bulkrna-cosinor-rhythm/bulkrna_cosinor_rhythm.py \
  --input <data.ext> --output results/ \
  --method fixed-period-cosinor-ols

Dependencies

Python packages this skill's script needs. They are not installed for you — check before a long run.

numpy, pandas, matplotlib

Files

SKILL.md and 19 other files (references) in skills/bulkrna/run-derived/bulkrna-cosinor-rhythm of TianGzlab/OmicsClaw.

SKILL.md
_api.py
bulkrna_cosinor_rhythm.py
completion_report.json
data/demo_input.csv
examples/example_step.py
manifest.json
references/acquisition_abstraction.json
references/admission.md
references/methodology.md
references/output_contract.md
references/parameter_lift.md
references/parameters.md
references/r_visualization.md
references/source_completion_report.json
references/source_manifest.json
references/source_result_summary.md
scaffold_spec.json
… and 2 more

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Bulkrna Cosinor Rhythm 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 Cosinor Rhythm compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Bulkrna Cosinor Rhythm this skillTianGzlab/OmicsClaw	161	—	~840	Automated safety check: Pass	Apache-2.0	3 days ago
Ukb Ppp Region FetchClawBio/ClawBio	1.2k	—	~4.6k	Automated safety check: Pass	MIT	2 days ago
Spatial XeniumQING1105/ezST	101	—	~535	Automated safety check: Pass	MIT	1 mo ago
Cerna Analysisaipoch/medical-research-skills	1.9k	—	~2.4k	Automated safety check: Pass	MIT	24 days ago
Bio Proteomics Spectral LibrariesGPTomics/bioSkills	1.2k	1 repos	~4.6k	Automated safety check: Pass	MIT	1 mo ago
Plannotate Plasmid Annotationjaechang-hits/SciAgent-Skills	374	1 repos	~4.7k	Automated safety check: Pass	GPL-3.0	12 days ago

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Questions about Bulkrna Cosinor Rhythm

What does Bulkrna Cosinor Rhythm do?

Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV. Bulkrna Cosinor Rhythm is an agent skill from TianGzlab/OmicsClaw. Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.

When should I use Bulkrna Cosinor Rhythm?

Bulkrna Cosinor Rhythm fits situations like: needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV; tasks that involve Bioinformatics; tasks that involve CSV and tabular files.

How do I install Bulkrna Cosinor Rhythm in Claude Code?

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

How do I install Bulkrna Cosinor Rhythm in Codex?

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

Can I use Bulkrna Cosinor Rhythm 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-cosinor-rhythm -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-cosinor-rhythm, .gemini/skills/bulkrna-cosinor-rhythm, .github/skills/bulkrna-cosinor-rhythm and .opencode/skills/bulkrna-cosinor-rhythm in your project.

What does Bulkrna Cosinor Rhythm need to run?

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

Does Bulkrna Cosinor Rhythm 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 Cosinor Rhythm 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 Cosinor Rhythm use?

Bulkrna Cosinor Rhythm 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 Cosinor Rhythm use?

About 840 tokens (SKILL.md is roughly 3.4k 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 19k tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Cosinor Rhythm?

Skills that share tags, products or a category with Bulkrna Cosinor Rhythm: Ukb Ppp Region Fetch (ClawBio/ClawBio, 1.2k stars), Spatial Xenium (QING1105/ezST, 101 stars), Cerna Analysis (aipoch/medical-research-skills, 1.9k stars) and Bio Proteomics Spectral Libraries (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bulkrna Cosinor Rhythm?

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 Cosinor Rhythm

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

bulkrna-cosinor-rhythm

Purpose

Inputs & Outputs

API

fit(timecourse)

run_info(result, *, keep=True)

rhythm_figure(result)

Flow

Gotchas

Key CLI

See also

Dependencies

Files

Compare with similar skills

Similar skills

More from TianGzlab/OmicsClaw

Related

Questions about Bulkrna Cosinor Rhythm

`fit(timecourse)`

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

`rhythm_figure(result)`