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 AndyZhuang/Opentest --skill bioinformaticsgit clone --depth 1 https://github.com/AndyZhuang/OpentestWrote 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/andyzhuang/opentest/bioinformatics)<a href="https://agentmods.dev/skills/andyzhuang/opentest/bioinformatics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/bioinformatics/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/andyzhuang/opentest/bioinformatics"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/bioinformatics.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 | $0.00000 | $0.00518 |
| Opus 5 | $0.00000 | $0.00259 |
| Sonnet 5 | $0.00000 | $0.00104 |
| Haiku 4.5 | $0.00000 | $0.00052 |
Grade A, and why
bioinformatics 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
100% identical to bioinformatics — 0 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.
What it actually says
Bioinformatics Analysis
Overview
Computational biology and genomics analysis pipelines. GENERAL: not locked to any specific tool — use Scanpy, Seurat, DESeq2, or any appropriate package.
Common Workflows
RNA-seq Analysis
- Quality control (FastQC, MultiQC)
- Alignment (STAR, HISAT2) or pseudo-alignment (Salmon, kallisto)
- Quantification (featureCounts, Salmon quant)
- Normalization (DESeq2 vst/rlog, edgeR TMM)
- Differential expression (DESeq2, edgeR, limma-voom)
- Visualization (volcano plot, MA plot, heatmap)
- Pathway analysis (clusterProfiler GO/KEGG, GSEA)
scRNA-seq Analysis (Scanpy / Seurat)
- Quality control (filter cells: mito%, gene count, UMI count)
- Normalization (library size, log1p)
- Feature selection (highly variable genes)
- Dimensionality reduction (PCA → UMAP/tSNE)
- Clustering (Leiden, Louvain)
- Marker identification (Wilcoxon, t-test)
- Cell type annotation (manual markers or automated)
- Trajectory analysis (PAGA, diffusion pseudotime)
GWAS / Genomics
- Quality control (MAF, HWE, call rate, relatedness)
- Association testing (PLINK, REGENIE)
- Multiple testing correction (Bonferroni, FDR)
- Manhattan plot, Q-Q plot
- Fine-mapping, colocalization
Key Databases
- GEO (Gene Expression Omnibus): public expression datasets
- TCGA (The Cancer Genome Atlas): cancer genomics
- GTEx (Genotype-Tissue Expression): tissue-specific expression
- ClinVar: clinical variant interpretations
- UniProt: protein sequences and annotations
- Ensembl: genome annotation
File Formats
| Format | Content | Tools |
|---|---|---|
| FASTQ | Raw sequencing reads | FastQC, Trimmomatic |
| BAM/SAM | Aligned reads | samtools, IGV |
| VCF | Variant calls | bcftools, GATK |
| h5ad | AnnData (scRNA-seq) | Scanpy |
| RDS | R object | Seurat, DESeq2 |
| BED | Genomic regions | bedtools |
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 · 51 lines · 0 tokens per session scan A f60535f6e2eb
bioinformatics is a skill published in the GitHub repository AndyZhuang/Opentest (22 stars, last pushed 6mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 518 tokens. A static security scan graded it A with 0 findings. It is 100% identical to bioinformatics, differing in 0 lines, and is treated as a copy.
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