{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T20:38:59Z","timestamp":1771274339578,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,11,25]],"date-time":"2023-11-25T00:00:00Z","timestamp":1700870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32CA257923"],"award-info":[{"award-number":["T32CA257923"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020600","name":"University of Florida Informatics Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020600","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Experimental methods using microRNA\/target ligation have recently provided significant insights into microRNA functioning through generation of chimeric (hybrid) RNA sequences. Here, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence data in the \u201chyb\u201d file format to enable customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes a suite of python objects for developing custom analyses of hybrid data as well as miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA\/target interactions in Vienna format.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Hybkit is provided free and open source under the GNU GPL license at github.com\/RenneLab\/hybkit and archived on Zenodo (doi.org\/10.5281\/zenodo.7834299). Hybkit distributions are also provided via PyPI (pypi.org\/project\/hybkit), Conda (bioconda.github.io\/recipes\/hybkit\/README.html), and Docker (quay.io\/repository\/biocontainers\/hybkit).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad721","type":"journal-article","created":{"date-parts":[[2023,11,25]],"date-time":"2023-11-25T13:47:43Z","timestamp":1700920063000},"source":"Crossref","is-referenced-by-count":5,"title":["Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0649-9506","authenticated-orcid":false,"given":"Daniel","family":"Stribling","sequence":"first","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States"},{"name":"UF Genetics Institute, University of Florida , Gainesville, FL 32610, United States"},{"name":"UF Health Cancer Center, University of Florida , Gainesville, FL 32610, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5715-6717","authenticated-orcid":false,"given":"Lauren A","family":"Gay","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7391-8806","authenticated-orcid":false,"given":"Rolf","family":"Renne","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States"},{"name":"UF Genetics Institute, University of Florida , Gainesville, FL 32610, United States"},{"name":"UF Health Cancer Center, University of Florida , Gainesville, FL 32610, United 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