AR
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arxiv-database
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Data & Repro
BI
bio-crispr-screens-library-design
Maintainer FreedomIntelligence · Last updated April 1, 2026
CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference screens.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-crispr-screens-library-design
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: CRISPOR-based scoring with BioPython for sequence handling.
- Design a custom CRISPR library for my screen" → Select optimal sgRNAs for knockout, CRISPRi/a, or base editing libraries with on-target scoring, off-target filtering, and control guide design. Python: CRISPOR-based scoring with BioPython for sequence handling.
- def design_cas12a_guides(gene_sequence, n_guides=4): pam_pattern = 'TTT[ACG]' # TTTV guide_length = 23.
- for match in re.finditer(f'({pam_pattern})([ACGT]{{{guide_length}}})', gene_sequence): pam = match.group(1) guide = match.group(2) # Cas12a cuts downstream of guide #...
Source Doc
Excerpt From SKILL.md
sgRNA Selection Criteria
Goal: Score and rank candidate sgRNAs for a target gene based on design quality metrics.
Approach: Scan the gene sequence for PAM sites, extract 20-nt protospacer sequences, score each on GC content, poly-T avoidance, 5' G preference, and length, then return the top-ranked candidates.
Library Composition
Goal: Assemble a complete sgRNA library targeting a list of genes with appropriate controls.
Approach: Design top-scoring guides for each gene, append non-targeting, essential-control, and safe-harbor-control guides, and compile into an ordered library table.
Control Guide Design
Goal: Design control guide sets for normalization and quality assessment in CRISPR screens.
Approach: Generate random non-targeting sequences with acceptable GC content, add validated guides against known essential genes (positive controls) and safe-harbor loci (negative controls).
Use cases
- Use when designing custom sgRNA libraries for knockout, activation, or interference screens.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- mageck-analysis - Analyze screen results
- crispresso-editing - Validate editing efficiency
- screen-qc - QC sequencing data
- hit-calling - Identify screen hits
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