Awesome Regulatory Genomics: a curated catalog of tools for transcription-factor binding, motif and gene-regulatory analysis

A catalog of software tools, databases and methods for transcription-factor binding site prediction, sequence motif discovery and scanning, promoter and enhancer prediction, digital footprinting, ChIP-seq and ATAC-seq peak analysis, chromatin accessibility and nucleosomes, DNA methylation, the 3D genome, histone modifications, reporter assays, molecular QTL, regulatory variant interpretation and gene-regulatory network inference. The catalog is generated by a reproducible pipeline and then curated by hand. Records are harvested from bio.tools, filtered against a tiered EDAM-operation scheme that accounts for known annotation errors, enriched with source-repository activity and OpenAlex citation counts, and extended by hand with tools bio.tools does not index. Three properties distinguish it from a hand-typed list. Citation counts are verified rather than inherited, since a publication identifier that resolves can still be the wrong paper; where several tools share a platform paper no count is shown rather than crediting each with the platform's total. Records that were considered and excluded are published with the reason, so the scope boundary can be argued with rather than guessed at. And the whole catalog rebuilds from committed data with no network access and no API key. Archived here are the catalog itself (data/catalog.json, data/catalog.tsv), the records excluded from it with their reasons (data/excluded.tsv), the hand-written curation layer, and the pipeline that produces them.