{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:19:10Z","timestamp":1792790350561,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,21]]},"group-title":"Bioinformatics","reference-count":0,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","award":["R01HD112559"],"award-info":[{"award-number":["R01HD112559"]}],"id":[{"id":"https:\/\/ror.org\/04byxyr05","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","award":["R01HD105734"],"award-info":[{"award-number":["R01HD105734"]}],"id":[{"id":"https:\/\/ror.org\/04byxyr05","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","award":["R01HD094937"],"award-info":[{"award-number":["R01HD094937"]}],"id":[{"id":"https:\/\/ror.org\/04byxyr05","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,21]]},"abstract":"<jats:p>Motivation\nSingle-cell RNA sequencing (scRNA-seq) cluster annotation is a critical step in data analysis. Current methods are time-consuming, difficult to reproduce, or limited in tissue or species coverage.  \n\nResults\nWe developed celltypeEnrich, a cluster-level annotation tool that uses a hypergeometric test to identify enrichment of cell-type-specific genes from input gene lists. Enrichment results from up to 26 reference datasets are used to determine a consensus annotation. Benchmarking using scRNA-seq datasets from three tissues spanning two species showed 62-72% annotation accuracy for celltypeEnrich, generally outperforming other tools, which had either lower accuracy, incomplete tissue coverage, or the need for parameter optimization. The performance of celltypeEnrich remained stable when input gene lists were down-sampled to 25% of their original size.\n\nAvailability and Implementation\ncelltypeEnrich is freely available at (https:\/\/celltypeenrich.gdcb.iastate.edu) as an R Shiny web application under the MIT license for non-profit academic use.<\/jats:p>","DOI":"10.64898\/2026.09.15.751735","type":"posted-content","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T15:30:12Z","timestamp":1790004612000},"source":"Crossref","is-referenced-by-count":0,"title":["celltypeEnrich: a consensus-based scRNA-seq cluster annotation tool"],"prefix":"10.64898","author":[{"given":"Sabrena","family":"Rutledge","sequence":"first","affiliation":[{"name":"Iowa State University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geetu","family":"Tuteja","sequence":"additional","affiliation":[{"name":"Iowa State University"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.15.751735","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T15:30:12Z","timestamp":1790004612000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.15.751735"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,21]]},"references-count":0,"URL":"https:\/\/doi.org\/10.64898\/2026.09.15.751735","relation":{},"subject":[],"published":{"date-parts":[[2026,9,21]]},"subtype":"preprint"}}