AI peer review for genomics and epigenetics papers

PerfectPaper reviews genomics, epigenetics and metabolism manuscripts with a standing team of specialist agents, and lets you add up to three custom agents of your own for the conventions that team does not cover. This page contains five prebuilt agent briefs for omics work: multiple testing and enrichment, data availability and accessions, batch effects and replicate structure, metabolomics reporting, and variant nomenclature. Each is a text brief you copy into the agent field.

The standing team already covers statistics, methodology, figures, tables, citations and prior work. The five below exist because omics manuscripts fail for reasons that are specific to the assay rather than to statistics in general, and a generalist reviewer does not know to look for them.

The five agents

Multiple testing and enrichment discipline — nominal p-values reported without correction, enrichment run against the wrong background universe, ranking metric unstated. The most common reason an omics paper draws a methods objection.

Data availability and accessions — missing GEO, SRA, dbGaP or MetaboLights accessions, unstated genome build, absent tool versions and parameters. The most common reason an omics paper is returned before review.

Batch effects and replicate structure — batch confounded with condition, batch never modelled, technical replicates presented as biological.

Metabolomics and flux reporting — normalisation and internal standards unstated, no natural-abundance correction on isotope tracing, identification confidence level never given.

Variant and gene nomenclature — non-HGVS variant strings, unversioned transcript references, deprecated gene symbols.

How custom agents work

You can add up to three custom agents to a review. Each takes a name, a set of instructions up to 6,000 characters, a work type, a skill level, and an optional set of tools — web search, scholarly search, code execution, and vision for figure reading. The instructions are yours; PerfectPaper supplies the review contract and output format around them, so a brief describes what to look for rather than how to format findings.

Three slots is a real constraint, which is why these briefs are narrow. An agent asked to check everything checks nothing in particular.

Choosing among them

For a sequencing paper with a differential expression result, the multiple testing agent earns its slot first, then batch effects. For a paper being prepared for submission rather than revised, data availability moves first, because it is the check that prevents a return without review. For metabolomics, take the metabolomics agent and one of the other two. Variant nomenclature is worth a slot only when the paper reports specific variants, in which case it is fast and unambiguous.

Review my manuscript

Frequently asked questions

How many custom agents can I add to one review?

Three. Each has its own name, instructions, work type, skill level and tool selection, and they run alongside the standing specialist team rather than replacing any part of it.

Do I have to write my own agent instructions?

No. The five briefs in this cluster are complete and can be pasted in unchanged. PerfectPaper can also suggest an agent for your specific paper based on its title and abstract, which you can then edit.

Will a custom agent duplicate the built-in review?

It can, which is why these briefs say what the standing team already covers. The standing team includes statistics, causal inference, methodology, figures, tables and citation verification, so a custom agent is best spent on a convention specific to your assay or field.

Can a custom agent search the literature?

Yes, if you give it the scholarly search or web search tools. Two of the briefs in this cluster use them; the others are better without, because a checking task is more reliable when it reads only the manuscript.

Does a custom agent cost extra?

Custom agents run as part of the review rather than as a separate charge. Adding three does not cost more than adding none.