Chdb Datastore
vemetric/vemetric
A skill your agent uses when the user has tabular data (pandas DataFrame, parquet, csv, Arrow, json) and wants to filter, group, aggregate, join, or speed up slow pandas.
Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests.
Install Bulkrna Survival
$ npx skills add TianGzlab/OmicsClaw --skill bulkrna-survival -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-survival --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/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bulkrna/bulkrna-survival .claude/skills/bulkrna-survival && 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 "bulkrna-survival" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-survival into .claude/skills/bulkrna-survival/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-survival", 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/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-survivalType 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 TianGzlab/OmicsClaw --skill bulkrna-survival -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-survival --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bulkrna/bulkrna-survival .agents/skills/bulkrna-survival && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bulkrna-survival" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-survival into .agents/skills/bulkrna-survival/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-survival", 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 TianGzlab/OmicsClaw --skill bulkrna-survival -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-survival --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bulkrna/bulkrna-survival .cursor/skills/bulkrna-survival && 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 "bulkrna-survival" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-survival into .cursor/skills/bulkrna-survival/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-survival", 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/TianGzlab/OmicsClaw.git --path skills/bulkrna/bulkrna-survival--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 TianGzlab/OmicsClaw --skill bulkrna-survival -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-survival --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bulkrna/bulkrna-survival .gemini/skills/bulkrna-survival && 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 "bulkrna-survival" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-survival into .gemini/skills/bulkrna-survival/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-survival", 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 TianGzlab/OmicsClaw bulkrna-survivalInstalls 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 TianGzlab/OmicsClaw --skill bulkrna-survival -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bulkrna/bulkrna-survival .github/skills/bulkrna-survival && 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 "bulkrna-survival" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-survival into .github/skills/bulkrna-survival/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-survival", 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 TianGzlab/OmicsClaw --skill bulkrna-survival -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-survival --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bulkrna/bulkrna-survival .opencode/skills/bulkrna-survival && 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 "bulkrna-survival" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-survival into .opencode/skills/bulkrna-survival/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-survival", 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-survival- GitHub stars
- 161
- Token cost
- ~1.2k tokens
- SKILL.md length
- 485 words
- Files
- 9 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests.
- Tasks that involve DataFrames
- SKILL.md covers When to use, Use from a step, API and Methods and parameters, plus 5 more sections
- Runs Python and R scripts from its folder; calls python
What it does
Bulkrna Survival is an agent skill from TianGzlab/OmicsClaw. Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests. R survival also fits Cox HR; Python reports a descriptive events/person-time ratio. Skip missing clinical outcomes.
Its SKILL.md is about 1.2k 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_survival.py` and `examples/example_step.py`).
It sits in Data & Analytics, covering DataFrames. It works with 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 Apache-2.0.
When your agent uses it
- Tasks that involve DataFrames
Example prompts
- “/bulkrna-survival”
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 and R), 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 Survival loads about 1.2k tokens when it runs, and up to ~1.7k if it reads all its reference files. Until then it costs about 62 tokens; SKILL.md has 485 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 TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 485 words, ~1,237 tokens.
Download SKILL.mdSave it as
.claude/skills/bulkrna-survival/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.- name
- bulkrna-survival
- description
- Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests. R survival also fits Cox HR; Python reports a descriptive events/person-time ratio. Skip missing clinical outcomes.
- trigger
- survival, Kaplan-Meier, Cox, prognosis, hazard ratio, overall survival, clinical outcome
- tags
- bulkrna, survival, Kaplan-Meier, Cox, hazard-ratio, clinical
bulkrna-survival
When to use
Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests. R survival also fits Cox HR; Python reports a descriptive events/person-time ratio. Skip missing clinical outcomes.
Use from a step
from skills._sdk.notebook import load_skill, write_output
library = load_skill("bulkrna-survival")
result = library.analyze(data, clinical=clinical, backend="python")
write_output(result, "tables/result.csv")
write_output(library.curve_figure(result, gene="G"), "figures/result.png")Read expression and metadata with read_input before calling the library.
examples/example_step.py constructs a small synthetic dataset and checks
its results through the step runner and fresh-kernel replay.
API
<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->analyze(data: pd.DataFrame, *, clinical: pd.DataFrame, genes: list[str] | None=None, cutoff_method: str='median', backend: str='auto') -> pd.DataFrame
Return gene-wise survival comparisons without modifying expression.
:param data: Nonnegative feature-by-sample expression. :param clinical: Clinical table with unique sample, nonnegative time and binary event columns. :param genes: Genes to test; None uses every row. Missing genes raise. :param cutoff_method: CLI default median; optimal scans cuts with unadjusted p-values. :param backend: auto prefers R survival with Cox HR, as the CLI did; python uses an events/person-time ratio. :returns: Per-gene table with diagnostics and KM points attached in attrs. :raises ValueError: Identifiers, clinical values, requested genes or comparison groups are invalid. :raises ImportError: Explicit R backend lacks survival or Matrix. :raises RuntimeError: The requested R method fails or returns incomplete results.
run_info(data: pd.DataFrame, *, keep: bool=True) -> dict
Return actual backend, HR estimator and summary.
:param data: Result from analyze. :param keep: Keep diagnostics by default; the CLI passes False. :returns: Diagnostics dictionary. :raises ValueError: The table has no analysis diagnostics.
km_table(data: pd.DataFrame) -> pd.DataFrame
Return the fitted Kaplan-Meier points for both expression strata.
:param data: Result from analyze. :returns: New table with gene, group, time and survival columns. :raises ValueError: The result lacks stored curves.
curve_figure(data: pd.DataFrame, *, gene: str)
Plot the stored Kaplan-Meier curves for one analyzed gene.
:param data: Result from analyze. :param gene: Exact gene identifier in the result. :returns: Matplotlib Figure. :raises ValueError: No curve exists for the requested gene.
<!-- api:end -->Show full SKILL.md (187 more words)Show less
Methods and parameters
The function library returns DataFrames and Figures. The CLI loads the same library and owns reports and file writes. R runs in a temporary directory using Matrix Market, feature/sample identifiers and metadata. No R intermediate is a permanent CLI output.
Gotchas
analyze(backend="auto")prefers R survival, which fits Cox PH hazard ratios. Its Python fallback uses a descriptive events/person-time ratio.run_info()["hazard_estimator"]distinguishes them.analyzeraises for missing genes or insufficient high/low groups; it does not silently deliver a subset of the requested genes.analyze(cutoff_method="optimal")scans cutoffs and reports unadjusted p-values. Treat the selected-cutoff test as exploratory.km_tableexposes both KM curves. Median survival is None when a curve never reaches 0.5; no extrapolated median is invented.run_info()["dropped_expression_samples"]reports samples excluded by the expression/clinical intersection. Clinical IDs must be unique.
Inputs and outputs
Feature-by-sample expression CSV and a clinical CSV containing unique sample, nonnegative time and binary event.
CLI outputs:
tables/survival_results.csvfigures/km_<gene>.pngper successful genefigures/forest_plot.pngwhen at least two genes succeedreport.md,result.jsonreproducibility/commands.sh
CLI
python skills/bulkrna/bulkrna-survival/bulkrna_survival.py --demo --output /tmp/bulkrna_survival_demoRun the script with --help for real-input arguments.
See also
references/parameters.mdreferences/methodology.mdreferences/output_contract.md
Dependencies
matplotlib, numpy, pandas, scipy, survival, Matrix
© TianGzlab, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 8 other files (references) in skills/bulkrna/bulkrna-survival of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- bulkrna_survival.py
- examples/example_step.py
- references/methodology.md
- references/output_contract.md
- references/parameters.md
- rscripts/bulkrna_survival.R
- tests/test_api.py
Open the folder on GitHubat commit 90a3bec
Compare with similar skills
Bulkrna Survival 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 |
|---|---|---|---|---|---|---|
| Bulkrna Survival this skillTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Chdb Datastorevemetric/vemetric | 395 | 2 repos | ~1.4k | Automated safety check: Pass | Apache-2.0 | |
| Polar Python SDKpolarsource/polar | 10k | — | ~1.8k | Automated safety check: Pass | Apache-2.0 | |
| CSV Data Summarizercoffeefuelbump/csv-data-summarizer-claude-skill | 468 | 2 repos | ~1.4k | Automated safety check: Pass | None | |
| Pandas ProJeffallan/claude-skills | 12k | 1 repos | ~1.5k | Automated safety check: Pass | MIT | |
| Python Executorcortega26/chile-hub | 113 | 2 repos | ~1.5k | Automated safety check: Pass | MIT |
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Bulkrna Deconvolution
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Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.
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Related
Works with
Categories
Questions about Bulkrna Survival
What does Bulkrna Survival do?
Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests. Bulkrna Survival is an agent skill from TianGzlab/OmicsClaw. Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests.
When should I use Bulkrna Survival?
Bulkrna Survival fits situations like: tasks that involve DataFrames.
How do I install Bulkrna Survival in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill bulkrna-survival -a claude-code`. Or copy the skill folder (skills/bulkrna/bulkrna-survival in TianGzlab/OmicsClaw) into .claude/skills/bulkrna-survival in your project. Claude Code loads it when a task matches its description.
How do I install Bulkrna Survival in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill bulkrna-survival -a codex`. Or copy the skill folder (skills/bulkrna/bulkrna-survival in TianGzlab/OmicsClaw) into .agents/skills/bulkrna-survival in your project. Codex loads it when a task matches its description.
Can I use Bulkrna Survival 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-survival -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-survival, .gemini/skills/bulkrna-survival, .github/skills/bulkrna-survival and .opencode/skills/bulkrna-survival in your project.
What does Bulkrna Survival need to run?
Going by SKILL.md and its folder, Bulkrna Survival needs Python and R for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Bulkrna Survival 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 Survival 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 Survival use?
Bulkrna Survival 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 Survival use?
About 1.2k tokens (SKILL.md is roughly 4.9k 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 449 tokens, read only when the agent opens those files.
What are the alternatives to Bulkrna Survival?
Skills that share tags, products or a category with Bulkrna Survival: Chdb Datastore (vemetric/vemetric, 395 stars), Polar Python SDK (polarsource/polar, 10k stars), CSV Data Summarizer (coffeefuelbump/csv-data-summarizer-claude-skill, 468 stars) and Pandas Pro (Jeffallan/claude-skills, 12k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bulkrna Survival?
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.