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Agent skill

Bulkrna Batch Correction

by TianGzlab in TianGzlab/OmicsClaw

Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Batch Correction

skills CLI
$ npx skills add TianGzlab/OmicsClaw --skill bulkrna-batch-correction -a claude-code

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

GitHub CLI
$ gh skill install TianGzlab/OmicsClaw bulkrna-batch-correction --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-batch-correction .claude/skills/bulkrna-batch-correction && 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/

Facts

Skill name
bulkrna-batch-correction
GitHub stars
161
Token cost
~1.2k tokens
SKILL.md length
450 words
Files
9 (incl. references)
Skills in repo
88
Repo updated
First seen
Licence
Apache-2.0

At a glance

Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.

  • 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 and R scripts from its folder; calls python
  • Tasks that involve DataFrames

What it does

Bulkrna Batch Correction is an agent skill from TianGzlab/OmicsClaw. Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation. Skip single-batch inputs; use sc-batch-integration for single-cell data or spatial-integrate for spatial slices.

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_batch_correction.py` and `examples/example_step.py`).

It sits in Research & Science, covering Bioinformatics and 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 Bioinformatics
  • Tasks that involve DataFrames

Example prompts

  • “/bulkrna-batch-correction”

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 Batch Correction 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 64 tokens; SKILL.md has 450 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
~1.2k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.7k

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). 450 words, ~1,200 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-batch-correction/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.
name
bulkrna-batch-correction
description
Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation. Skip single-batch inputs; use sc-batch-integration for single-cell data or spatial-integrate for spatial slices.
trigger
batch correction, ComBat, batch effect, harmonize, multi-cohort, batch removal
tags
bulkrna, batch-correction, ComBat, harmonization, batch-effect

bulkrna-batch-correction

When to use

Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation. Skip single-batch inputs; use sc-batch-integration for single-cell data or spatial-integrate for spatial slices.

Use from a step

python
from skills._sdk.notebook import load_skill, write_output
library = load_skill("bulkrna-batch-correction")
result = library.correct(data, batches=batches, backend="python")
write_output(result, "tables/result.csv")
write_output(library.pca_figure(result, batches=batches), "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 -->
correct(data: pd.DataFrame, *, batches: pd.DataFrame, mode: str='parametric', backend: str='auto') -> pd.DataFrame

Return corrected expression, leaving the input unchanged.

:param data: Finite nonnegative expression, features by samples; correction uses this scale directly. :param batches: Metadata with sample and batch columns, and optional biological condition. :param mode: CLI default parametric, or non-parametric (requires R sva). :param backend: auto prefers R as the CLI did; r requires R, python uses the legacy parametric approximation. :returns: Corrected DataFrame with run_info diagnostics; values can be negative. :raises ValueError: Data, metadata, mode or backend is invalid. :raises ImportError: An explicitly requested R backend is unavailable. :raises RuntimeError: R fails and the requested mode/design has no Python fallback.

run_info(data: pd.DataFrame, *, keep: bool=True) -> dict

Return backend diagnostics and before/after batch metrics.

:param data: Result of correct. :param keep: Keep diagnostics by default; the CLI passes False. :returns: Diagnostics dictionary. :raises ValueError: No correction diagnostics are attached.

pca_figure(data: pd.DataFrame, *, batches: pd.DataFrame)

Plot PCA after signed log2(1+abs(x)), accepting negative corrections.

:param data: Original or corrected feature-by-sample expression. :param batches: Metadata containing sample and batch. :returns: Matplotlib Figure. :raises ValueError: Samples lack batch metadata.

<!-- api:end -->
Show full SKILL.md (202 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

  • correct(backend="auto") prefers R sva and warns/records any Python fallback. backend="r" requires R. The Python method is the legacy parametric approximation, not numerical equivalence to sva.
  • correct requires at least two batches and two samples per batch. Missing labels and single-batch inputs raise before any backend runs.
  • correct applies ComBat directly to the supplied scale, not to an automatic log transform. Outputs may be negative and are not integer counts for DESeq2.
  • correct(mode="non-parametric") and condition covariates require R; Python cannot silently substitute a different design or mode.
  • run_info()["summary"] contains before/after PCA silhouette metrics using signed log2(1+abs(x)), so negative corrections remain finite. Inspect condition-by-batch balance before removing effects.

Inputs and outputs

Expression CSV with feature identifiers in the first column; metadata CSV with sample and batch, plus optional condition.

CLI outputs:

  • tables/corrected_expression.csv
  • tables/batch_metrics.csv
  • figures/pca_before_correction.png
  • figures/pca_after_correction.png
  • figures/batch_assessment.png
  • report.md, result.json
  • reproducibility/commands.sh

CLI

bash
python skills/bulkrna/bulkrna-batch-correction/bulkrna_batch_correction.py --demo --output /tmp/bulkrna_batch_correction_demo

Run the script with --help for real-input arguments.

See also

  • references/parameters.md
  • references/methodology.md
  • references/output_contract.md

Dependencies

matplotlib, numpy, pandas, scipy, sva, 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-batch-correction of TianGzlab/OmicsClaw.

  • SKILL.md
  • _api.py
  • bulkrna_batch_correction.py
  • examples/example_step.py
  • references/methodology.md
  • references/output_contract.md
  • references/parameters.md
  • rscripts/combat.R
  • tests/test_api.py

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Bulkrna Batch Correction 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 Batch Correction compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bulkrna Batch Correction this skillTianGzlab/OmicsClaw161—~1.2kAutomated safety check: PassApache-2.0
Bio Proteomics Spectral LibrariesGPTomics/bioSkills1.2k1 repos~4.6kAutomated safety check: PassMIT
Bio Expression Matrix Sparse HandlingGPTomics/bioSkills1.2k1 repos~5.6kAutomated safety check: PassMIT
deepTools NGS Toolkitdavila7/claude-code-templates32k13 repos~4.5kAutomated safety check: PassMIT
PyDESeq2 Differential Expressiondavila7/claude-code-templates32k12 repos~4kAutomated safety check: PassMIT
Gtars Genomic Interval Toolkitdavila7/claude-code-templates32k12 repos~1.9kAutomated safety check: PassMIT

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Works with

Categories

Questions about Bulkrna Batch Correction

What does Bulkrna Batch Correction do?

Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation. Bulkrna Batch Correction is an agent skill from TianGzlab/OmicsClaw. Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.

When should I use Bulkrna Batch Correction?

Bulkrna Batch Correction fits situations like: tasks that involve Bioinformatics; tasks that involve DataFrames.

How do I install Bulkrna Batch Correction in Claude Code?

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

How do I install Bulkrna Batch Correction in Codex?

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

Can I use Bulkrna Batch Correction 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-batch-correction -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-batch-correction, .gemini/skills/bulkrna-batch-correction, .github/skills/bulkrna-batch-correction and .opencode/skills/bulkrna-batch-correction in your project.

What does Bulkrna Batch Correction need to run?

Going by SKILL.md and its folder, Bulkrna Batch Correction 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 Batch Correction 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 Batch Correction 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 Batch Correction use?

Bulkrna Batch Correction 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 Batch Correction use?

About 1.2k tokens (SKILL.md is roughly 4.8k 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 469 tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Batch Correction?

Skills that share tags, products or a category with Bulkrna Batch Correction: Bio Proteomics Spectral Libraries (GPTomics/bioSkills, 1.2k stars), Bio Expression Matrix Sparse Handling (GPTomics/bioSkills, 1.2k stars), deepTools NGS Toolkit (davila7/claude-code-templates, 32k stars) and PyDESeq2 Differential Expression (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bulkrna Batch Correction?

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.