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 GPTomics/bioSkills --skill allele-specific-bindinggit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/allele-specific-binding)<a href="https://agentmods.dev/skills/gptomics/bioskills/allele-specific-binding"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/allele-specific-binding/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/gptomics/bioskills/allele-specific-binding"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/allele-specific-binding.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 | $0.00150 | $0.04136 |
| Opus 5 | $0.00075 | $0.02068 |
| Sonnet 5 | $0.00030 | $0.00827 |
| Haiku 4.5 | $0.00015 | $0.00414 |
Grade A, and why
bio-chipseq-allele-specific-binding 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 6d 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-chipseq-allele-specific-binding — 94% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 311 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: WASP 0.3.4+, RASQUAL 1.1+, BaalChIP 1.30+ (Bioconductor), AlleleSeq 2.0+, samtools 1.19+, bcftools 1.19+, GATK 4.5+, pysam 0.22+.
Allele-Specific Binding (ASB)
"Identify variants that affect transcription factor or histone modification binding in cis" -> Compare ChIP-seq read counts at the reference and alternate alleles of heterozygous variants in a single sample. Differential read counts (ALT vs REF at hetSNPs in peaks) reveal allele-specific binding.
- CLI (mandatory bias filter): WASP
mapping pipelineto remove reference-allele mapping bias - CLI (joint association): RASQUAL for cis-QTL + ASB (genotype VCF piped in via tabix)
- R (Bayesian beta-binomial): BaalChIP with copy-number-aware overdispersion
- CLI (personalized genome): AlleleSeq with phased diploid genome
- Statistical test: beta-binomial likelihood ratio or chi-squared on count tables
ASB analysis has three universal pitfalls: reference-allele mapping bias (universal across short-read aligners), imprinted loci (constitutively allele-skewed by biology), and copy-number variation (changes effective allele dose). All three must be addressed or results are unreliable.
Method Taxonomy
| Method | Year | Approach | Strength | Fails when |
|---|---|---|---|---|
| WASP (van de Geijn 2015) | 2015 | Map reads, swap alleles, re-map, drop discordant | Universal first step; aligner-agnostic; mandatory preprocessing | Drops 22-31% of reads; reduces power; not an analysis method itself |
| RASQUAL (Kumasaka 2016) | 2016 | Joint genotype-phenotype association with per-feature phi bias parameter |
Improves QTL mapping; integrates bias correction; works for ChIP/ATAC/RNA-seq | Computationally intensive; assumes binomial bias structure |
| BaalChIP (de Santiago 2017) | 2017 | Bayesian beta-binomial; copy-number-aware overdispersion | Cancer genomes (copy-number imbalance); rigorous inference | Slower; assumes copy-number known |
| AlleleSeq (Rozowsky 2011) | 2011 | Personalized diploid genome alignment | Avoids reference bias completely; conceptually cleanest | Requires phased genotype + diploid genome construction; computational cost |
| MBASED (Mayba 2014) | 2014 | Meta-analysis-based ASE; gene-level | RNA-seq oriented; adapted for ChIP gene-body binning | Gene-level not peak-level; less precise for narrow TF peaks |
| AllelicImbalance (R package) | — | Bioconductor multi-method | Easy R workflow | Requires variants and BAM; less rigorous than BaalChIP |
| deepSEA / chromBPNet variant effects | 2015 / 2024 | Deep-learning predictions | Sequence-only; no chromatin sample needed | Predictive not measurement; see chip-deep-learning |
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.
- 6d ago First seen · 311 lines · 150 tokens per session scan A b09597e490f2
bio-chipseq-allele-specific-binding is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 25d ago), licensed MIT. It adds 150 tokens to every session and 4,136 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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