Analytical Operators in Cross-Scale Genomics: Estimands, Analysis Order, and Inference

Code and supporting configuration files for the Review “

Analytical Operators in Cross-Scale Genomics: Estimands, Analysis Order, and Inference

”.

This software release contains the custom Python and R code used for the automated and descriptive literature-mapping components of the Review, including PubMed, Europe PMC and OpenAlex retrieval; record harmonization and exact-identifier deduplication; machine-generated scale and analytical-operator labels; bibliometric summary tables; sensitivity summaries; and generation of the literature-landscape panels reported in Supplementary Figure S9.

The automated labels are used for retrieval prioritization and descriptive mapping only. They do not represent a manually validated systematic-review inclusion classification and should not be interpreted as reproducing a completed PRISMA evidence set. Scientific claims in the accompanying Review are grounded in the cited literature and worked methodological examples.

The release also contains configuration dictionaries, structured seed evidence, reproducibility tests and documentation. Private API credentials are not included. External retrieval services are subject to provider availability, rate limits and future API changes; therefore, exact historical record counts are best reproduced using the archived summary data supplied with the manuscript.

Associated manuscript: Analytical operators in genome-wide inference: an estimand-centered framework across biological scales.