{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T07:18:03Z","timestamp":1773904683213,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T00:00:00Z","timestamp":1696464000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01 DK132320"],"award-info":[{"award-number":["R01 DK132320"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Kansas Center for Metabolism and Obesity REsearch"},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Science","doi-asserted-by":"crossref","award":["P20 GM144269"],"award-info":[{"award-number":["P20 GM144269"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cancer Center Support","award":["P30 CA168524"],"award-info":[{"award-number":["P30 CA168524"]}]},{"name":"Kansas Institute for Precision Medicine COBRE"},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Science","doi-asserted-by":"crossref","award":["P20 GM130423"],"award-info":[{"award-number":["P20 GM130423"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100018524","name":"Kansas IDEA Network of Biomedical Research Excellence","doi-asserted-by":"publisher","award":["P20 GM103418"],"award-info":[{"award-number":["P20 GM103418"]}],"id":[{"id":"10.13039\/100018524","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The Tapestri platform offers DNA and protein analysis at the single-cell level. Integrating both types of data is beneficial for studying multiple cell populations in heterogeneous microenvironments, such as tumor tissues. Here, we present optima, an R package for the processing and analysis of data generated from the Tapestri platform. This package provides streamlined functionality for raw data filtering, integration, normalization, transformation, and visualization. Insights gained from the optima package help users to identify unique cell populations and uncover surface protein expression patterns. The results generated by optima help researchers elucidate dynamic changes at the single-cell level in heterogeneous microenvironments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>This package is available in Github: https:\/\/github.com\/rachelgriffard\/optima.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad611","type":"journal-article","created":{"date-parts":[[2023,10,4]],"date-time":"2023-10-04T20:18:27Z","timestamp":1696450707000},"source":"Crossref","is-referenced-by-count":3,"title":["optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8367-729X","authenticated-orcid":false,"given":"Dong","family":"Pei","sequence":"first","affiliation":[{"name":"Department of Biostatistics & Data 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