New: 98,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Bulkrna Read Qc

by TianGzlab in TianGzlab/OmicsClaw

Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq.

Apache-2.0Auto-check passedResearch & Science

Install Bulkrna Read Qc

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

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

GitHub CLI
$ gh skill install TianGzlab/OmicsClaw bulkrna-read-qc --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-qc .claude/skills/bulkrna-read-qc && 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-qc
GitHub stars
161
Token cost
~1.1k tokens
SKILL.md length
420 words
Files
8 (incl. references)
Skills in repo
88
Repo updated
First seen
Licence
Apache-2.0

At a glance

Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment 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
  • Tasks that involve DataFrames

What it does

Bulkrna Read Qc is an agent skill from TianGzlab/OmicsClaw. Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq. Skip when reads are already aligned (use bulkrna-read-alignment); counted (use bulkrna-qc); single-cell FASTQ (use sc-fastq-qc).

Its SKILL.md is about 1.1k 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_read_qc.py` and `examples/example_step.py`).

It sits in Research & Science, covering Bioinformatics and DataFrames. 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-read-qc”

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 Qc loads about 1.1k tokens when it runs, and up to ~1.4k if it reads all its reference files. Until then it costs about 62 tokens; SKILL.md has 420 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~62
When it runs · the whole SKILL.md, loaded when a task matches
~1.1k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.4k

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). 420 words, ~1,132 tokens.

Download SKILL.mdSave it as .claude/skills/bulkrna-read-qc/SKILL.md (or your agent's skills folder). This skill also uses 7 other files; get the full folder from GitHub.
name
bulkrna-read-qc
description
Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq. Skip when reads are already aligned (use bulkrna-read-alignment); counted (use bulkrna-qc); single-cell FASTQ (use sc-fastq-qc).
trigger
FASTQ QC, read quality, Phred, FastQC, adapter, GC content, Q20, Q30
tags
bulkrna, FASTQ, QC, Phred, GC-content, adapter, read-quality

bulkrna-read-qc

When to use

Read raw Phred+33 FASTQ before alignment. This implements selected quality metrics, not the complete FastQC suite. Use bulkrna-read-alignment for logs.

Use from a step

python
from skills._sdk.notebook import load_skill, write_output
library = load_skill('bulkrna-read-qc')
data = library.demo_data(random_state=42)
result = library.quality_control(data)
write_output(result, 'tables/qc_summary.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_fastq(path: str | Path, *, max_reads: int=100000) -> pd.DataFrame

Read FASTQ records; pass this function as reader= to read_input.

:param path: FASTQ path; a .gz suffix selects gzip decompression. :param max_reads: CLI limit 100000; increase for a larger leading-read sample. :returns: Sequence and Phred+33 quality strings as rows. :raises ValueError: Records are truncated, malformed, or have unequal sequence/quality lengths.

quality_control(reads: pd.DataFrame, *, max_reads: int=100000) -> pd.DataFrame

Compute a new one-row quality summary for Phred+33 reads.

:param reads: sequence and quality string columns; input rows are not changed. :param max_reads: CLI default 100000 leading records; increase to inspect more reads. :returns: Scalar QC metrics and adapter counts; run_info retains per-base distributions. :raises ValueError: Reads, lengths or Phred+33 scores are invalid.

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

Read full quality distributions and sampling diagnostics.

:param result: Output of quality_control. :param keep: True preserves attrs; False removes diagnostics before serialization. :returns: A separate dictionary containing metrics and sampling provenance. :raises TypeError: The result is not a DataFrame.

quality_figure(result: pd.DataFrame)

Plot mean and interquartile quality by read position.

:param result: QC result retaining its diagnostic attrs. :returns: A matplotlib Figure without writing files. :raises KeyError: Per-base diagnostics are absent.

Show full SKILL.md (187 more words)Show less
gc_figure(result: pd.DataFrame)

Plot GC fractions across sampled reads.

:param result: QC result retaining its diagnostic attrs. :returns: A matplotlib Figure without writing files. :raises KeyError: GC diagnostics are absent.

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

Generate valid synthetic FASTQ records in memory.

:param random_state: CLI seed 42; change for another simulation without altering global RNG state. :returns: Five thousand 150-base reads with quality strings of the same length. :raises ValueError: The seed is invalid.

<!-- api:end -->

Methods and parameters

read_fastq reads the leading 100000 records by default and accepts .gz. quality_control computes per-base quality, Q20/Q30, GC, lengths and adapter motif hits from sequence/quality strings. It does not trim reads.

Gotchas

  • read_fastq rejects truncated FASTQ and unequal sequence/quality lengths.
  • quality_control assumes Phred+33, not the older Phred+64 encoding.
  • adapter_rate sums motif hits and can exceed 100% if a read contains multiple adapters.

Inputs and outputs

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

  • tables/qc_summary.csv
  • figures/per_base_quality.png
  • figures/gc_content.png
  • figures/read_length_distribution.png
  • figures/quality_score_distribution.png
  • report.md
  • result.json
  • reproducibility/commands.sh
  • demo_reads.fastq only with --demo.

CLI

bash
python skills/bulkrna/bulkrna-read-qc/bulkrna_read_qc.py --demo --output /tmp/bulkrna_read_qc

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 7 other files (references) in skills/bulkrna/bulkrna-read-qc of TianGzlab/OmicsClaw.

  • SKILL.md
  • _api.py
  • bulkrna_read_qc.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 Read Qc 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 Qc compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bulkrna Read Qc this skillTianGzlab/OmicsClaw161—~1.1kAutomated safety check: PassApache-2.0
ArboretoK-Dense-AI/scientific-agent-skills48k1 repos~2.7kAutomated safety check: PassBSD-3-Clause
Bio Proteomics Spectral LibrariesGPTomics/bioSkills1.2k1 repos~4.6kAutomated safety check: PassMIT
Arboreto Grn Inferencejaechang-hits/SciAgent-Skills3742 repos~5.3kAutomated safety check: PassBSD-3-Clause
Lamindb Data Managementjaechang-hits/SciAgent-Skills3742 repos~4kAutomated safety check: PassApache-2.0
Bio Expression Matrix Sparse HandlingGPTomics/bioSkills1.2k1 repos~5.6kAutomated safety check: PassMIT

Similar skills

  • Arboreto

    K-Dense-AI/scientific-agent-skills

    Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.

    48k GitHub starsUsed in 1 repo~2.7k tokens
    Research & ScienceAuto-check passed

  • Bio Proteomics Spectral Libraries

    GPTomics/bioSkills

    Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relative intensities, normalized RT, optional CCS), covering experimental DDA…

    1.2k GitHub starsUsed in 1 repo~4.6k tokens
    Research & ScienceAuto-check passed

  • Arboreto Grn Inference

    jaechang-hits/SciAgent-Skills

    GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest).

    374 GitHub starsUsed in 2 repos~5.3k tokens
    Research & ScienceAuto-check passed

  • Lamindb Data Management

    jaechang-hits/SciAgent-Skills

    Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills.

    374 GitHub starsUsed in 2 repos~4k tokens
    Research & ScienceAuto-check passed

  • Bio Expression Matrix Sparse Handling

    GPTomics/bioSkills

    Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit…

    1.2k GitHub starsUsed in 1 repo~5.6k tokens
    Research & ScienceAuto-check passed

  • Bio Proteomics Dia Analysis

    GPTomics/bioSkills

    Analyzes data-independent acquisition (DIA) proteomics by scoring reconstructed fragment-chromatogram peak groups against a decoy null with DIA-NN (library-free directDIA, library-based, or…

    1.2k GitHub starsUsed in 1 repo~5.4k tokens
    Research & ScienceAuto-check passed

More from TianGzlab/OmicsClaw

All 88 skills in this repo

  • Bulkrna Cosinor Rhythm

    TianGzlab/OmicsClaw

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

    161 GitHub stars~840 tokensUpdated 3 days ago
    Auto-check passed

  • Bulkrna Batch Correction

    TianGzlab/OmicsClaw

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

    161 GitHub stars~1.2k tokensUpdated 3 days ago
    Auto-check passed

  • Bulkrna Coexpression

    TianGzlab/OmicsClaw

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

    161 GitHub stars~1.3k tokensUpdated 3 days ago
    Auto-check passed

  • Bulkrna De

    TianGzlab/OmicsClaw

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

    161 GitHub stars~867 tokensUpdated 3 days ago
    Auto-check passed

  • Bulkrna Deconvolution

    TianGzlab/OmicsClaw

    Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.

    161 GitHub stars~757 tokensUpdated 3 days ago
    Auto-check passed

  • Bulkrna Enrichment

    TianGzlab/OmicsClaw

    Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list.

    161 GitHub stars~860 tokensUpdated 3 days ago
    Auto-check passed

Categories

Questions about Bulkrna Read Qc

What does Bulkrna Read Qc do?

Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq. Bulkrna Read Qc is an agent skill from TianGzlab/OmicsClaw. Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq.

When should I use Bulkrna Read Qc?

Bulkrna Read Qc fits situations like: tasks that involve Bioinformatics; tasks that involve DataFrames.

How do I install Bulkrna Read Qc in Claude Code?

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

How do I install Bulkrna Read Qc in Codex?

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

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

What does Bulkrna Read Qc need to run?

Going by SKILL.md and its folder, Bulkrna Read Qc 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 Qc 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 Qc 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 Qc use?

Bulkrna Read Qc 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 Qc use?

About 1.1k tokens (SKILL.md is roughly 4.5k 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 302 tokens, read only when the agent opens those files.

What are the alternatives to Bulkrna Read Qc?

Skills that share tags, products or a category with Bulkrna Read Qc: Arboreto (K-Dense-AI/scientific-agent-skills, 48k stars), Bio Proteomics Spectral Libraries (GPTomics/bioSkills, 1.2k stars), Arboreto Grn Inference (jaechang-hits/SciAgent-Skills, 374 stars) and Lamindb Data Management (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 Read Qc?

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.