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Agent skill

Crispr Screen Triage

by ClawBio in ClawBio/ClawBio

Deterministic CRISPR screen hit ranking from local guide-level count tables

MITAuto-check passedResearch & Science

Install Crispr Screen Triage

skills CLI
$ npx skills add ClawBio/ClawBio --skill crispr-screen-triage -a claude-code

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

GitHub CLI
$ gh skill install ClawBio/ClawBio crispr-screen-triage --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/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/crispr-screen-triage .claude/skills/crispr-screen-triage && 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
crispr-screen-triage
GitHub stars
1.2k
Used in
1 other repo
Token cost
~1.7k tokens
SKILL.md length
623 words
Files
4
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Deterministic CRISPR screen hit ranking from local guide-level count tables

  • Works in 4 steps: Count validation: Requires guide ID,… → Guide aggregation: Computes guide-level… → Local triage: Computes a fixed gene… → …
  • Tasks that involve Bioinformatics
  • SKILL.md covers Trigger, Why This Exists, Core Capabilities and Scope, plus 17 more sections
  • Runs Python scripts from its folder; calls python

What it does

Crispr Screen Triage is an agent skill from ClawBio/ClawBio. Deterministic CRISPR screen hit ranking from local guide-level count tables

Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `crispr_screen_triage.py` and `tests/test_crispr_screen_triage.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “/crispr-screen-triage”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

  1. Count validation: Requires guide ID, gene, control count, treatment count, essentiality, and druggability.
  2. Guide aggregation: Computes guide-level log2 fold change and aggregates by gene using the median.
  3. Local triage: Computes a fixed gene triage score from depletion plus user-supplied essentiality and druggability.
  4. Report pack: Writes report, JSON, gene/guide CSVs, and reproducibility command.

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. 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

Crispr Screen Triage loads about 1.7k tokens when it runs. Until then it costs about 24 tokens; SKILL.md has 623 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~24
When it runs · the whole SKILL.md, loaded when a task matches
~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 ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 623 words, ~1,737 tokens.

Download SKILL.mdSave it as .claude/skills/crispr-screen-triage/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
crispr-screen-triage
description
Deterministic CRISPR screen hit ranking from local guide-level count tables
license
MIT
metadata.version
0.1.0
metadata.author
ClawBio
metadata.domain
functional-genomics
metadata.tags
crispr, screen, triage

CRISPR Screen Triage

You are CRISPR Screen Triage, a specialised ClawBio agent for ranking gene-level CRISPR screen hits from supplied guide counts and annotations.

Trigger

Fire this skill when the user says any of:

  • "triage CRISPR screen hits"
  • "rank guide-level CRISPR counts"
  • "rank depleted CRISPR genes"
  • "score genes from a knockout screen"
  • "which CRISPR hits should I follow up"

Do NOT fire when:

  • The user asks for variant interpretation.
  • The user asks for single-cell clustering.
  • The user asks for clinical actionability.

Why This Exists

  • Without it: Users sort fold changes manually and ignore follow-up feasibility.
  • With it: Depletion, essentiality, and druggability are combined deterministically.
  • Why ClawBio: The score is transparent, local, and reproducible.

Core Capabilities

  1. Count validation: Requires guide ID, gene, control count, treatment count, essentiality, and druggability.
  2. Guide aggregation: Computes guide-level log2 fold change and aggregates by gene using the median.
  3. Local triage: Computes a fixed gene triage score from depletion plus user-supplied essentiality and druggability.
  4. Report pack: Writes report, JSON, gene/guide CSVs, and reproducibility command.

Scope

One skill, one task. This skill ranks gene hits from guide-level screen counts and does not design guides, perform statistical screen calling, fetch external annotations, or claim therapy suitability. The essentiality and druggability columns must already be present in the input table. They are not fetched from DepMap, Open Targets, ChEMBL, or any other service.

Input Formats

FormatExtensionRequired FieldsExample
CSV.csvguide_id, gene, control_count, treatment_count, essentiality, druggabilitydemo_screen_counts.csv

essentiality and druggability are user-supplied downstream annotations. This skill only averages and weights them after guide-level depletion is calculated.

Workflow

  1. Validate: Confirm required columns and numeric counts/scores.
  2. Compute: Calculate guide-level log2((treatment + 1) / (control + 1)).
  3. Aggregate: Collapse guides to genes using median log2 fold change and mean annotations.
  4. Triage: Score depletion, druggability, and essentiality with fixed weights.
  5. Report: Write ranked markdown, JSON, gene table, guide table, and command trace.

CLI Reference

bash
python skills/crispr-screen-triage/crispr_screen_triage.py --input counts.csv --output /tmp/crispr
python skills/crispr-screen-triage/crispr_screen_triage.py --demo --output /tmp/crispr
python clawbio.py run crispr-triage --demo

Demo

bash
python clawbio.py run crispr-triage --demo

Expected output: a synthetic twelve-guide, six-gene ranked report with BRCA1 as the top hit.

Algorithm / Methodology

  1. Guide depletion: Convert each treatment/control guide count pair to log2 fold change.
  2. Gene aggregation: Use median guide log2FC per gene so one noisy guide cannot dominate.
  3. Score: 0.55 * max(0, -median_log2FC) + 0.25 * druggability + 0.20 * essentiality.
  4. Priority: High requires score >= 1.35 and median log2FC <= -1.0.
  5. Non-goal: This is not a canonical statistical screen caller. It does not model negative-binomial counts, copy number, or Bayesian essentiality.
Show full SKILL.md (220 more words)Show less

Example Queries

  • "Rank these CRISPR hits"
  • "Triage depleted genes from this screen"
  • "Which knockout hits are most follow-up ready?"

Example Output

markdown
# CRISPR Screen Triage Report

| Rank | Gene | Guides | Median log2FC | Priority |
|---:|---|---:|---:|---|
| 1 | BRCA1 | 2 | -2.66 | high |

Output Structure

output_directory/
├── report.md
├── result.json
├── tables/
│   ├── triaged_genes.csv
│   └── guide_metrics.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256

Dependencies

  • Python 3.11+ and the standard library only.

Gotchas

  • Do not treat the priority score as validation: It is a triage score only.
  • Do not call external databases: Demo and tests must remain deterministic.
  • Do not mix guide-level and gene-level semantics: Input uses guide-level counts plus user-supplied gene annotations.

Safety

  • Local-first: No external APIs or uploads.
  • Disclaimer: Every report includes the ClawBio medical disclaimer.
  • Audit trail: Commands are written to reproducibility/commands.sh.

Agent Boundary

The agent dispatches and explains. The Python skill scores and writes outputs.

Integration with Bio Orchestrator

Trigger conditions: CRISPR screen, depleted genes, knockout hit ranking.

Chaining Partners

  • target-validation-scorer: downstream target evidence synthesis.
  • omics-target-evidence-mapper: cross-omics support for top hits.

Maintenance

  • Review cadence: Re-evaluate weights quarterly.
  • Staleness signals: Repo adds guide-level statistical screen-calling support.
  • Deprecation: Archive if replaced by a full screen-analysis workflow.

Author & Attribution

Prepared by Mrinal Joshi, Imperial College London and UK Dementia Research Institute, using his functional-genomics and bioinformatics background to scope a local deterministic CRISPR hit triage helper. The implementation is intentionally a transparent downstream ranker over supplied counts and annotations, not a canonical screen-scoring method.

Citations

  • ClawBio local deterministic triage rules in crispr_screen_triage.py; this skill does not claim a method-paper implementation.

© ClawBio, MIT. 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 3 other files in skills/crispr-screen-triage of ClawBio/ClawBio.

  • SKILL.md
  • crispr_screen_triage.py
  • demo_screen_counts.csv
  • tests/test_crispr_screen_triage.py

Open the folder on GitHubat commit dece754

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Crispr Screen Triage 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.

Crispr Screen Triage compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Crispr Screen Triage this skillClawBio/ClawBio1.2k1 repos~1.7kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Crispr Screen Triage

What does Crispr Screen Triage do?

Deterministic CRISPR screen hit ranking from local guide-level count tables. Crispr Screen Triage is an agent skill from ClawBio/ClawBio.

When should I use Crispr Screen Triage?

Crispr Screen Triage fits situations like: tasks that involve Bioinformatics.

How do I install Crispr Screen Triage in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill crispr-screen-triage -a claude-code`. Or copy the skill folder (skills/crispr-screen-triage in ClawBio/ClawBio) into .claude/skills/crispr-screen-triage in your project. Claude Code loads it when a task matches its description.

How do I install Crispr Screen Triage in Codex?

Run `npx skills add ClawBio/ClawBio --skill crispr-screen-triage -a codex`. Or copy the skill folder (skills/crispr-screen-triage in ClawBio/ClawBio) into .agents/skills/crispr-screen-triage in your project. Codex loads it when a task matches its description.

Can I use Crispr Screen Triage 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 ClawBio/ClawBio --skill crispr-screen-triage -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/crispr-screen-triage, .gemini/skills/crispr-screen-triage, .github/skills/crispr-screen-triage and .opencode/skills/crispr-screen-triage in your project.

What does Crispr Screen Triage need to run?

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

Does Crispr Screen Triage 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 Crispr Screen Triage 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 Crispr Screen Triage use?

Crispr Screen Triage is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Crispr Screen Triage use?

About 1.7k tokens (SKILL.md is roughly 6.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Crispr Screen Triage?

Skills that share tags, products or a category with Crispr Screen Triage: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Crispr Screen Triage?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 8, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.