{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:10Z","timestamp":1772138050933,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T00:00:00Z","timestamp":1646870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"AIRC Foundation for Cancer Research in Italy [AIRC","award":["21837"],"award-info":[{"award-number":["21837"]}]},{"name":"National Cancer Institute of the National Institutes of Health","award":["2U24CA180996"],"award-info":[{"award-number":["2U24CA180996"]}]},{"name":"Chan Zuckerberg Initiative DAF","award":["CZF2019-002443"],"award-info":[{"award-number":["CZF2019-002443"]}]},{"name":"Silicon Valley Community Foundation and by University of Padova Strategic Research Infrastructure Grant 2017"},{"name":"CAPRI: Calcolo ad Alte Prestazioni per la Ricerca e l\u2019Innovazione"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present NewWave, a scalable R\/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA sequencing data. To achieve scalability, NewWave uses mini-batch optimization and can work with out-of-memory data, enabling users to analyze datasets with millions of cells.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>NewWave is implemented as an open-source R package available through the Bioconductor project at https:\/\/bioconductor.org\/packages\/NewWave\/<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac149","type":"journal-article","created":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T15:13:57Z","timestamp":1646752437000},"page":"2648-2650","source":"Crossref","is-referenced-by-count":8,"title":["<i>NewWave<\/i>\n                    : a scalable R\/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3722-0472","authenticated-orcid":false,"given":"Federico","family":"Agostinis","sequence":"first","affiliation":[{"name":"Department of Biology, Universit\u00e0 degli Studi di Padova , Padova 35100, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4792-9047","authenticated-orcid":false,"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[{"name":"Department of Biology, Universit\u00e0 degli Studi di Padova , Padova 35100, Italy"}]},{"given":"Gabriele","family":"Sales","sequence":"additional","affiliation":[{"name":"Department of Biology, Universit\u00e0 degli Studi di Padova , Padova 35100, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8508-5012","authenticated-orcid":false,"given":"Davide","family":"Risso","sequence":"additional","affiliation":[{"name":"Department of Statistical Science, Universit\u00e0 degli studi di Padova , Padova 35100, Italy"}]}],"member":"286","published-online":{"date-parts":[[2022,3,10]]},"reference":[{"key":"2023041402562215300_","author":"Pag\u00e8s","year":"2021"},{"key":"2023041402562215300_","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/s13059-020-02128-7","article-title":"Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis","volume":"21","author":"Raimundo","year":"2020","journal-title":"Genome Biol"},{"key":"2023041402562215300_","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1038\/s41467-017-02554-5","article-title":"A general and flexible method for signal extraction from single-cell RNA-seq data","volume":"9","author":"Risso","year":"2018","journal-title":"Nat. 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