15 Agent Skills Design and Analyze CRISPR Screens, From Library to Hit Genes

[Mutation Technology Publications]

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​

Skill	What it does
bagel-essentiality	Finds essential genes in Cas9 fitness screens with BAGEL2 Bayes factors
base-editing-analysis	Analyzes base-editing screens for variant function
batch-correction	Corrects batch effects with ComBat, RUV, SVA or control-sgRNA normalization
combinatorial-screens	Designs and analyzes paired-Cas9 and multiplexed Cas12a screens
copy-number-correction	Removes the gene-independent copy-number artifact in Cas9 screens
crispresso-editing	Quantifies editing outcomes (indels, HDR, base and prime edits) with CRISPResso2
drugz-chemogenomic	Analyzes drug-modifier screens with drugZ
hit-calling	A decision tree for picking the right hit-calling method
in-vivo-screens	Designs and analyzes screens in tumor models, organoids and adoptive transfers
jacks-analysis	Runs JACKS to model per-sgRNA efficacy across screens
library-design	Designs sgRNA libraries for knockout, CRISPRi, CRISPRa and Cas12a
mageck-analysis	Runs MAGeCK from counts through RRA and MLE analysis
perturb-seq-analysis	Analyzes Perturb-seq, CROP-seq and ECCITE-seq single-cell screens
prime-editing-screens	Designs and analyzes pooled prime-editor screens for precise variants
screen-qc	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.