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Agent skill

Bulkrna Splicing

by TianGzlab in TianGzlab/OmicsClaw

Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Splicing

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

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

GitHub CLI
$ gh skill install TianGzlab/OmicsClaw bulkrna-splicing --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-splicing .claude/skills/bulkrna-splicing && 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-splicing
GitHub stars
161
Token cost
~822 tokens
SKILL.md length
247 words
Files
10 (incl. references)
Skills in repo
88
Repo updated
First seen
Licence
Apache-2.0

At a glance

Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events.

  • 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 Splicing is an agent skill from TianGzlab/OmicsClaw. Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events. Skip when you only have count-level DE (use bulkrna-de); splicing in single-cell; spatial data (currently unsupported).

Its SKILL.md is about 820 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_splicing.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-splicing”

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 Splicing loads about 822 tokens when it runs, and up to ~1.9k if it reads all its reference files. Until then it costs about 65 tokens; SKILL.md has 247 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~65
When it runs · the whole SKILL.md, loaded when a task matches
~822
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). 247 words, ~822 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-splicing/SKILL.md (or your agent's skills folder). This skill also uses 9 other files; get the full folder from GitHub.
name
bulkrna-splicing
description
Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events. Skip when you only have count-level DE (use bulkrna-de); splicing in single-cell; spatial data (currently unsupported).
trigger
alternative splicing, splicing analysis, PSI, rMATS, SUPPA2, exon skipping, differential splicing
tags
bulkrna, splicing, alternative-splicing, PSI, rMATS, SUPPA2

bulkrna-splicing

When to use

Summarize existing splicing tests; this skill does not call rMATS or SUPPA2. 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-splicing")
# Supply DataFrames read with read_input(..., reader=...) for your CSV layout.
result = library.summarize(events)
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 -->
summarize(events, *, dpsi_cutoff=0.1, padj_cutoff=0.05)

Summarize upstream event tests without changing the table.

:param events: DataFrame with gene, event_type, delta_psi and padj columns. :param dpsi_cutoff: CLI default 0.1; absolute delta-PSI must exceed it. :param padj_cutoff: CLI default 0.05; adjusted p values must be below it. :returns: Copy of events with diagnostics in attrs. :raises ValueError: Required columns, probabilities or thresholds are invalid.

run_info(result, *, keep=True)

Read event counts and threshold diagnostics.

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

significant_events(result)

Return events passing both strict thresholds.

:param result: DataFrame returned by summarize, with diagnostics retained. :returns: New filtered DataFrame. :raises KeyError: Diagnostics are absent.

volcano_figure(result)

Plot delta-PSI against upstream adjusted significance.

:param result: Event table with delta_psi and padj. :returns: A matplotlib Figure, without writing files. :raises KeyError: Required columns are absent.

<!-- api:end -->

Methods and parameters

See parameters and methodology.

Gotchas

  • summarize uses strict abs(delta_psi) > dpsi_cutoff and padj < padj_cutoff.
  • Rename upstream columns to gene, event_type, delta_psi, padj; summarize rejects missing fields.
  • significant_events filters supplied p values; it does not estimate significance.

Inputs and outputs

The library returns objects without file writes. CLI inventory:

Inputs

  • File types: .csv

Outputs

  • tables/significant_events.csv
  • tables/splicing_events.csv
  • figures/dpsi_distribution.png
  • figures/event_type_distribution.png
  • figures/volcano_splicing.png
  • report.md
  • result.json

CLI

bash
python skills/bulkrna/bulkrna-splicing/bulkrna_splicing.py --demo --output /tmp/bulkrna-splicing

See also

Dependencies

matplotlib, numpy, pandas, scipy

© 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 9 other files (references) in skills/bulkrna/bulkrna-splicing of TianGzlab/OmicsClaw.

  • SKILL.md
  • _api.py
  • bulkrna_splicing.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_splicing.py

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Bulkrna Splicing 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 Splicing compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bulkrna Splicing this skillTianGzlab/OmicsClaw161—~822Automated safety check: PassApache-2.0
Scanpy Single-Cell Analysisdavila7/claude-code-templates32k15 repos~2.8kAutomated safety check: PassMIT
deepTools NGS Toolkitdavila7/claude-code-templates32k12 repos~4.5kAutomated safety check: PassMIT
LaminDB Biological Data Managementdavila7/claude-code-templates32k12 repos~3.6kAutomated safety check: PassMIT
PyDESeq2 Differential Expressiondavila7/claude-code-templates32k11 repos~4kAutomated safety check: PassMIT
Gtars Genomic Interval Toolkitdavila7/claude-code-templates32k11 repos~1.9kAutomated safety check: PassMIT

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More from TianGzlab/OmicsClaw

All 88 skills in this repo

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

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  • Bulkrna Batch Correction

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  • Bulkrna Coexpression

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    Load when discovering bulk gene co-expression modules and hub genes with R WGCNA.

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  • Bulkrna De

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    Load when comparing gene expression between two conditions in bulk RNA-seq count data.

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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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  • Bulkrna Enrichment

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Categories

Questions about Bulkrna Splicing

What does Bulkrna Splicing do?

Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events. Bulkrna Splicing is an agent skill from TianGzlab/OmicsClaw. Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events.

When should I use Bulkrna Splicing?

Bulkrna Splicing fits situations like: tasks that involve Bioinformatics.

How do I install Bulkrna Splicing in Claude Code?

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

How do I install Bulkrna Splicing in Codex?

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

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

What does Bulkrna Splicing need to run?

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

Does Bulkrna Splicing 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 Splicing 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 Splicing use?

Bulkrna Splicing 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 Splicing use?

About 822 tokens (SKILL.md is roughly 3.3k 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 1.1k tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Splicing?

Skills that share tags, products or a category with Bulkrna Splicing: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), deepTools NGS Toolkit (davila7/claude-code-templates, 32k stars), LaminDB Biological Data Management (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 Splicing?

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.