Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PKU-YuanGroup/OpenAI4S --skill bio-crispr-screens-combinatorial-screensgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-crispr-screens-combinatorial-screens)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-crispr-screens-combinatorial-screens"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-crispr-screens-combinatorial-screens/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-crispr-screens-combinatorial-screens"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-crispr-screens-combinatorial-screens.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00252 | $0.04651 |
| Opus 5 | $0.00126 | $0.02325 |
| Sonnet 5 | $0.00050 | $0.00930 |
| Haiku 4.5 | $0.00025 | $0.00465 |
Grade A, and why
bio-crispr-screens-combinatorial-screens scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
97% identical to bio-crispr-screens-combinatorial-screens — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 273 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: MAGeCK 0.5.9+ (for MLE with interaction terms), Inzolia library annotation (Esmaeili Anvar 2024), pandas 2.2+, numpy 1.26+, scipy 1.12+, matplotlib 3.8+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
mageck --version;mageck mle --help - For Cas12a libraries: verify against published Inzolia / in4mer / Big Papi annotations
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Combinatorial CRISPR Screen Analysis
"Run a combinatorial CRISPR screen to find synthetic-lethal interactions" -> Design a paired or multiplex library, screen for double-knockout fitness, score per-pair genetic interaction (GI = observed_double - expected_additive), and identify synthetic-lethal (negative GI) and synthetic-rescue (positive GI) interactions.
- CLI:
mageck mlewith explicit interaction terms for paired-Cas9 (Big Papi-style) - Python: custom GI scoring for Cas12a multiplex (in4mer / Inzolia)
- Modality: enCas12a / LbCas12a single-array multiplex (preferred for paralog screens)
Combinatorial Architecture Decision Tree
| Goal | Architecture | Library | Why |
|---|---|---|---|
| Paralog buffering, identify synthetic lethal paralog pairs | enCas12a single-array 4-guide multiplex | Inzolia (Esmaeili Anvar 2024) | Cas9 single-KO misses paralog-buffered essentials (42% of constitutively expressed genes never score, Dede 2020) |
| Test specific pathway pair (e.g., DNA repair branches) | Big Papi (orthologous SaCas9 + SpCas9; two sgRNAs from U6 and H1 in pPapi) | Custom | Mature methodology; orthologous enzymes avoid repeated-element recombination |
| Combinatorial 3-way / 4-way knockout | in4mer (4-guide single Cas12a array) | Custom (in4mer) | Single transcript processed by Cas12a; multi-gene |
| Single-cell Perturb-seq with multi-pert per cell | Combinatorial Perturb-seq + Cas9 multiplex | Custom | Single-cell readout of multi-perturbation effects |
| Drug-modifier + KO interaction | Cas9 KO + drug treatment | Standard libraries | Drug as second "perturbation" |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 273 lines · 252 tokens per session scan A cddb4a95d7f2
bio-crispr-screens-combinatorial-screens is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 252 tokens to every session and 4,651 once invoked, about $0.0013 per session on Opus 5. A static security scan graded it A with 0 findings. It is 97% identical to bio-crispr-screens-combinatorial-screens, differing in 12 lines, and is treated as a copy.
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