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Agent skill

Bulkrna Geneid Mapping

by TianGzlab in TianGzlab/OmicsClaw

Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Geneid Mapping

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

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

GitHub CLI
$ gh skill install TianGzlab/OmicsClaw bulkrna-geneid-mapping --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-geneid-mapping .claude/skills/bulkrna-geneid-mapping && 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-geneid-mapping
GitHub stars
161
Token cost
~1.2k tokens
SKILL.md length
451 words
Files
8 (incl. references)
Skills in repo
88
Repo updated
First seen
Licence
Apache-2.0

At a glance

Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo 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 Geneid Mapping is an agent skill from TianGzlab/OmicsClaw. Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference. Skip when IDs already match downstream needs; use fetchmapping explicitly for MyGene lookup.

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 10 other files, including reference files (for example `_api.py`, `bulkrna_geneid_mapping.py` and `examples/example_step.py`).

It sits in Research & Science, covering Bioinformatics. It works with Ensembl and NCBI. 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-geneid-mapping”

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 Geneid Mapping loads about 1.2k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 63 tokens; SKILL.md has 451 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
~1.2k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.6k

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). 451 words, ~1,201 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-geneid-mapping/SKILL.md (or your agent's skills folder). This skill also uses 7 other files; get the full folder from GitHub.
name
bulkrna-geneid-mapping
description
Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference. Skip when IDs already match downstream needs; use fetch_mapping explicitly for MyGene lookup.
trigger
gene ID, Ensembl, Entrez, gene symbol, ID mapping, gene annotation, convert IDs
tags
bulkrna, gene-id, mapping, Ensembl, Entrez, HGNC, annotation

bulkrna-geneid-mapping

When to use

Convert Ensembl, Entrez and symbol identifiers in count-matrix row indexes. Use a caller-provided mapping for full coverage or non-human organisms. Skip when identifiers already match downstream needs.

Use from a step

python
import pandas as pd
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill('bulkrna-geneid-mapping')
data = read_input('counts.csv', reader=lambda path: pd.read_csv(path, index_col=0))
result = library.map_ids(data)
write_output(result, 'tables/result.csv')

examples/example_step.py runs offline and supports fresh-kernel replay. Pure computations return objects; CLI and steps own writes.

API

<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->
map_ids(data, *, from_type='ensembl', to_type='symbol', species='human', on_duplicate='sum', mapping=None)

Map count-matrix row identifiers without network or file access.

:param data: Gene-by-sample counts; the row index contains source IDs. :param from_type: CLI default ensembl; entrez and symbol are also supported. :param to_type: CLI default symbol; target namespace. :param species: CLI default human; mouse requires an explicit reference. :param on_duplicate: CLI default sum; first or drop resolve target collisions differently. :param mapping: Optional source/target DataFrame; None uses ten human demo genes only. :returns: A new mapped DataFrame with reference scope, mapping records and summary diagnostics. :raises ValueError: Namespaces, duplicate policy or reference data are invalid.

fetch_mapping(data, *, from_type='ensembl', to_type='symbol', species='human')

Query MyGene explicitly and return a local source/target mapping table.

:param data: Iterable of identifiers to send to the public MyGene service. :param from_type: Default ensembl; source namespace. :param to_type: Default symbol; requested target namespace. :param species: Default human; MyGene species selector. :returns: A DataFrame containing only identifiers for which MyGene returned a match. :raises ImportError: Install mygene with install_skill_deps if unavailable. :raises Exception: Network or service errors propagate; no demo substitute is returned.

mapping_table(data)

Return the original-to-target mapping decisions for every input row.

:param data: Mapped count matrix returned by map_ids. :returns: A new DataFrame with original_id, stripped_id, mapped_id and was_mapped. :raises KeyError: The count matrix has no mapping diagnostics.

Show full SKILL.md (185 more words)Show less
run_info(data, *, keep=True)

Read mapping diagnostics without modifying the count values.

:param data: Mapped counts returned by map_ids. :param keep: Default True; the CLI removes diagnostics with False. :returns: An independent diagnostic dictionary. :raises TypeError: data is not a DataFrame.

mapping_figure(data)

Plot mapped and unmapped source-row counts.

:param data: Count matrix returned by map_ids. :returns: A matplotlib Figure; no files are written. :raises KeyError: Mapping diagnostics are absent.

<!-- api:end -->

Methods and parameters

Local map_ids never queries the network. Its default reference contains ten human genes; it also supports reverse namespace mapping within that small reference. Pass a source/target DataFrame to override it. fetch_mapping explicitly sends identifiers to MyGene. The CLI queries MyGene only with --fetch-mygene.

Gotchas

  • map_ids strips Ensembl version suffixes, retains unmapped identifiers and resolves target collisions with sum, first or drop. Explicit mappings take priority. Non-human mapping without a reference raises an error. run_info identifies demo versus provided reference scope.

Inputs and outputs

tables/mapped_counts.csv, tables/mapping_table.csv, report.md, result.json and reproducibility/commands.sh. tables/unmapped_genes.csv is conditional on unmapped input rows. The CLI does not write figures.

CLI

bash
python skills/bulkrna/bulkrna-geneid-mapping/bulkrna_geneid_mapping.py --demo --output /tmp/bulkrna_geneid_mapping

See also

Dependencies

numpy, pandas, mygene, matplotlib

© 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 7 other files (references) in skills/bulkrna/bulkrna-geneid-mapping of TianGzlab/OmicsClaw.

  • SKILL.md
  • _api.py
  • bulkrna_geneid_mapping.py
  • examples/example_step.py
  • references/methodology.md
  • references/output_contract.md
  • references/parameters.md
  • tests/test_api.py

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Bulkrna Geneid Mapping 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 Geneid Mapping compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bulkrna Geneid Mapping this skillTianGzlab/OmicsClaw161—~1.2kAutomated safety check: PassApache-2.0
Tooluniverse Phylogeneticswu-yc/LabClaw1.1k2 repos~4.2kAutomated safety check: PassNone
Bio Ensembl RESTGPTomics/bioSkills1.2k2 repos~3.6kAutomated safety check: PassMIT
Ggetaipoch/medical-research-skills1.9k—~816Automated safety check: PassMIT
Gene Databasejaechang-hits/SciAgent-Skills3741 repos~4.4kAutomated safety check: PassCC0-1.0
Clinvar Databasejaechang-hits/SciAgent-Skills3741 repos~4.9kAutomated safety check: PassCC0-1.0

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Works with

Categories

Questions about Bulkrna Geneid Mapping

What does Bulkrna Geneid Mapping do?

Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference. Bulkrna Geneid Mapping is an agent skill from TianGzlab/OmicsClaw. Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference.

When should I use Bulkrna Geneid Mapping?

Bulkrna Geneid Mapping fits situations like: tasks that involve Bioinformatics.

How do I install Bulkrna Geneid Mapping in Claude Code?

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

How do I install Bulkrna Geneid Mapping in Codex?

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

Can I use Bulkrna Geneid Mapping 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-geneid-mapping -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-geneid-mapping, .gemini/skills/bulkrna-geneid-mapping, .github/skills/bulkrna-geneid-mapping and .opencode/skills/bulkrna-geneid-mapping in your project.

What does Bulkrna Geneid Mapping need to run?

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

Does Bulkrna Geneid Mapping 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 Geneid Mapping 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 Geneid Mapping use?

Bulkrna Geneid Mapping 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 Geneid Mapping 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 355 tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Geneid Mapping?

Skills that share tags, products or a category with Bulkrna Geneid Mapping: Tooluniverse Phylogenetics (wu-yc/LabClaw, 1.1k stars), Bio Ensembl REST (GPTomics/bioSkills, 1.2k stars), Gget (aipoch/medical-research-skills, 1.9k stars) and Gene Database (jaechang-hits/SciAgent-Skills, 374 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bulkrna Geneid Mapping?

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.