GPTomics' bioSkills includes 15 MIT-licensed skills for pooled CRISPR screens. They cover library design, QC, batch and copy-number correction, hit calling with MAGeCK, BAGEL2, JACKS and drugZ, and specialized screens: base editing, prime editing, combinatorial, in vivo and Perturb-seq. The skills cite the papers behind each method, so the agent can explain its choices.
All 15 install with one command from Cuttlefish.MD, HackerNoon's license-checked skills marketplace. They follow the open Agent Skills standard, so they run in Claude Code, Codex CLI and 30+ other tools, and each is indexed in HackerNoon's SKILL.md Library.
The 15 CRISPR screen skills
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Skill |
What it does |
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Finds essential genes in Cas9 fitness screens with BAGEL2 Bayes factors |
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Analyzes base-editing screens for variant function |
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Corrects batch effects with ComBat, RUV, SVA or control-sgRNA normalization |
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Designs and analyzes paired-Cas9 and multiplexed Cas12a screens |
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Removes the gene-independent copy-number artifact in Cas9 screens |
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Quantifies editing outcomes (indels, HDR, base and prime edits) with CRISPResso2 |
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Analyzes drug-modifier screens with drugZ |
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A decision tree for picking the right hit-calling method |
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Designs and analyzes screens in tumor models, organoids and adoptive transfers |
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Runs JACKS to model per-sgRNA efficacy across screens |
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Designs sgRNA libraries for knockout, CRISPRi, CRISPRa and Cas12a |
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Runs MAGeCK from counts through RRA and MLE analysis |
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Analyzes Perturb-seq, CROP-seq and ECCITE-seq single-cell screens |
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Designs and analyzes pooled prime-editor screens for precise variants |
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Checks library representation, Gini index, skew and replicate correlation |
For the full run from FASTQ to hit genes, the crispr-screen-pipeline workflow skill chains these together.
Install them
All 15 come with the Data & Science plugin, along with the rest of the 562 bioSkills:
/plugin marketplace add hackernoon/cuttlefish-agent-skills
/plugin install data-science@cuttlefish
For Codex CLI or another agent that supports the standard, clone the repo and copy plugins/data-science/skills/ into your agent's skills folder, such as .agents/skills/.
Each skill keeps its MIT license and an ATTRIBUTION.md crediting GPTomics and the source commit. Browse the full library at hackernoon.com/skills, and star Cuttlefish.MD on GitHub.