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Agent skill

Bulkrna Read Alignment

by TianGzlab in TianGzlab/OmicsClaw

Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Read Alignment

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

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

GitHub CLI
$ gh skill install TianGzlab/OmicsClaw bulkrna-read-alignment --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-read-alignment .claude/skills/bulkrna-read-alignment && 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-read-alignment
GitHub stars
161
Token cost
~1.3k tokens
SKILL.md length
488 words
Files
9 (incl. references)
Skills in repo
88
Repo updated
First seen
Licence
Apache-2.0

At a glance

Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq.

  • 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 Read Alignment is an agent skill from TianGzlab/OmicsClaw. Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq. Skip when data is raw FASTQ (use bulkrna-read-qc); already counted (use bulkrna-qc); genome-DNA alignment (use genomics-alignment).

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 11 other files, including reference files (for example `_api.py`, `bulkrna_read_alignment.py` and `examples/example_step.py`).

It sits in Research & Science, covering Bioinformatics. It works with Matplotlib. 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-read-alignment”

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 Read Alignment loads about 1.3k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 59 tokens; SKILL.md has 488 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~59
When it runs · the whole SKILL.md, loaded when a task matches
~1.3k
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). 488 words, ~1,278 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-read-alignment/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.
name
bulkrna-read-alignment
description
Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq. Skip when data is raw FASTQ (use bulkrna-read-qc); already counted (use bulkrna-qc); genome-DNA alignment (use genomics-alignment).
trigger
RNA-seq alignment, STAR, HISAT2, Salmon, mapping rate, read alignment, alignment QC
tags
bulkrna, alignment, STAR, HISAT2, Salmon, mapping-rate, strandedness

bulkrna-read-alignment

When to use

Summarize existing STAR, paired-end HISAT2 or Salmon logs. This does not run an aligner. Use bulkrna-read-qc for FASTQ and bulkrna-qc for counts.

Use from a step

python
from skills._sdk.notebook import load_skill, write_output
library = load_skill('bulkrna-read-alignment')
data = library.demo_data(random_state=42)
result = library.summarize(data)
write_output(result, 'tables/alignment_stats.csv')

For real files, pass read_fastq, read_log or read_reference as appropriate to read_input(..., reader=...). examples/example_step.py is executable.

API

<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->
read_log(path: str | Path) -> str

Read log text; pass this function as reader= to read_input.

:param path: STAR, HISAT2 or Salmon text/JSON log. :returns: File contents without interpreting its filename. :raises OSError: The file cannot be read.

summarize(data: str | pd.DataFrame, *, method: str='star') -> pd.DataFrame

Parse alignment counts and return a new mapping summary.

:param data: Log text or a one-row parsed table, including demo_data output. :param method: CLI default star; select hisat2 for paired-end summaries or salmon for meta_info JSON. :returns: Mapping counts/rates with quality heuristics in run_info; Salmon reports total mapped, not unique mapped. :raises ValueError: Required counts are missing, inconsistent or the method is unsupported.

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

Read mapping assessment and unavailable-evidence diagnostics.

:param result: Output of summarize. :param keep: True preserves attrs; False removes diagnostics before serialization. :returns: A separate quality/provenance dictionary. :raises TypeError: The result is not a DataFrame.

mapping_figure(result: pd.DataFrame)

Plot observed mapping counts as percentages.

:param result: Output of summarize. :returns: A matplotlib Figure without writing files. :raises KeyError: Mapping counts are absent.

composition_figure(result: pd.DataFrame)

Plot observed mapping composition.

:param result: Output of summarize. :returns: A matplotlib Figure without writing files. :raises KeyError: Mapping counts are absent.

coverage_figure(coverage: pd.DataFrame)

Plot an explicitly supplied gene-body coverage profile.

:param coverage: position and coverage columns; alignment logs cannot supply these observations. :returns: A matplotlib Figure without synthesizing missing measurements. :raises KeyError: Coverage columns are absent.

Show full SKILL.md (213 more words)Show less
demo_data(*, random_state: int=42) -> pd.DataFrame

Generate the synthetic STAR summary used by the CLI demo.

:param random_state: CLI seed 42; change for another simulation. :returns: One simulated alignment summary row. :raises ValueError: The seed is invalid.

demo_coverage(*, random_state: int=42) -> pd.DataFrame

Generate an illustrative coverage profile, not inferred from an alignment log.

:param random_state: CLI demo seed 42; change for another simulation. :returns: One hundred simulated percentile/coverage rows. :raises ValueError: The seed is invalid.

<!-- api:end -->

Methods and parameters

summarize defaults to STAR, matching the CLI. Choose hisat2 or salmon explicitly; filenames do not override that choice. STAR/HISAT2 include unique and multimapped counts. Salmon meta_info reports total mapped counts only.

Gotchas

  • summarize rejects absent or inconsistent read counts.
  • run_info states that logs provide neither gene-body coverage nor inferred strandedness.
  • coverage_figure needs an explicit measured profile. demo_coverage is synthetic and is only used by --demo.
  • mapped_rate for Salmon does not mean uniquely mapped rate.
  • HISAT2 unmapped is the residual after concordant pairs and includes discordant/unpaired mappings; run_info records this limitation.

Inputs and outputs

The CLI writes these artifacts; functions return DataFrames and Figures without writing them:

  • tables/alignment_stats.csv
  • figures/mapping_summary.png
  • figures/alignment_composition.png
  • figures/gene_body_coverage.png (demo only)
  • report.md
  • result.json
  • reproducibility/commands.sh

CLI

bash
python skills/bulkrna/bulkrna-read-alignment/bulkrna_read_alignment.py --demo --output /tmp/bulkrna_read_alignment

For real files use --input <file>; trajectory placement also needs --reference <file>.

See also

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

Dependencies

matplotlib, numpy, pandas

© 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-read-alignment of TianGzlab/OmicsClaw.

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

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Bulkrna Read Alignment 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 Read Alignment compared with similar skills
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Works with

Categories

Questions about Bulkrna Read Alignment

What does Bulkrna Read Alignment do?

Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq. Bulkrna Read Alignment is an agent skill from TianGzlab/OmicsClaw. Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq.

When should I use Bulkrna Read Alignment?

Bulkrna Read Alignment fits situations like: tasks that involve Bioinformatics.

How do I install Bulkrna Read Alignment in Claude Code?

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

How do I install Bulkrna Read Alignment in Codex?

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

Can I use Bulkrna Read Alignment 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-read-alignment -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-read-alignment, .gemini/skills/bulkrna-read-alignment, .github/skills/bulkrna-read-alignment and .opencode/skills/bulkrna-read-alignment in your project.

What does Bulkrna Read Alignment need to run?

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

Does Bulkrna Read Alignment 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 Read Alignment 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 Read Alignment use?

Bulkrna Read Alignment 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 Read Alignment use?

About 1.3k tokens (SKILL.md is roughly 5.1k 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 347 tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Read Alignment?

Skills that share tags, products or a category with Bulkrna Read Alignment: Bio Hi C Analysis Hic Visualization (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Restriction Mapping (GPTomics/bioSkills, 1.2k stars), Bio Copy Number Cnv Visualization (GPTomics/bioSkills, 1.2k stars) and Bio Data Visualization Manhattan Qq Locuszoom (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 Read Alignment?

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.