bio-workflows-crispr-editing-pipeline
End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.
npx skills add BioTender-max/awesome-bio-agent-skills --skill crispr-editing-pipeline --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, primer3-py 2.0+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # CRISPR Editing Pipeline **"Design a complete CRISPR editing experiment for my target gene"** → Orchestrate guide RNA design, off-target assessment, and strategy-specific template design (knockout, base editing, HDR knock-in, or prime editing) to produce delivery-ready constructs. Complete workflow for CRISPR experiment design: from target gene to delivery-ready constructs with branching paths for different editing strategies. ## Workflow Overview ``` Target Gene/Position | v [1. Guide RNA Design] --> CRISPRscan / Rule Set 2 / DeepCRISPR | v [2. Off-Target Assessment] --> Cas-OFFinder + CFD scoring | v Decision Point: What type of edit? | +---+-------------------+----------
- Version Compatibility
- Workflow Overview
- Prerequisites
- Primary Path: Gene Knockout
- Step 1: Guide RNA Design
- Step 2: Off-Target Assessment
- Step 3a: Knockout Design (Frameshift)
- Step 3b: Base Editing Design (CBE/ABE)
- Step 3c: Knockin Design (HDR Template)
- Visualization
- Parameter Recommendations
- Troubleshooting
- Output Files
- Related Skills
pip install crisprscan biopython pandas numpy matplotlib conda install -c bioconda primer3-py cas-offinder Python packages for scoring pip install crisprtools # if available
What does the bio-workflows-crispr-editing-pipeline skill do?
End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill crispr-editing-pipeline --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.