{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T02:40:37Z","timestamp":1774579237980,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T00:00:00Z","timestamp":1666396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Cancer Institute Clinical Proteomic Tumor Analysis Consortium","award":["U24CA210954"],"award-info":[{"award-number":["U24CA210954"]}]},{"name":"National Cancer Institute Clinical Proteomic Tumor Analysis Consortium","award":["U24CA271076"],"award-info":[{"award-number":["U24CA271076"]}]},{"DOI":"10.13039\/100004917","name":"CPRIT","doi-asserted-by":"publisher","award":["RR160027"],"award-info":[{"award-number":["RR160027"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cancer Prevention & Research Institutes of Texas"},{"name":"McNair Medical Institute at The Robert and Janice McNair Foundation"},{"name":"CPRIT Scholar in Cancer Research and a McNair"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>RNA-Seq and mass spectrometry-based studies generate omics data tables with measurements for tens of thousands of genes across all samples in a study. The success of a study relies on the quality of these data tables, which is determined by both experimental data generation and computational methods used to process raw experimental data into quantitative data tables. We present OmicsEV, an R package for the quality evaluation of omics data tables. For each data table, OmicsEV uses a series of methods to evaluate data depth, data normalization, batch effect, biological signal, platform reproducibility and multi-omics concordance, producing comprehensive visual and quantitative evaluation results that help assess the data quality of individual data tables and facilitate the identification of the optimal data processing method and parameters for the omics study under investigation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code and the user manual of OmicsEV are available at https:\/\/github.com\/bzhanglab\/OmicsEV, and the source code is released under the GPL-3 license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac698","type":"journal-article","created":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T12:57:49Z","timestamp":1666443469000},"page":"5463-5465","source":"Crossref","is-referenced-by-count":16,"title":["OmicsEV: a tool for comprehensive quality evaluation of omics data tables"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2261-3150","authenticated-orcid":false,"given":"Bo","family":"Wen","sequence":"first","affiliation":[{"name":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX 77030, USA"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9618-6011","authenticated-orcid":false,"given":"Eric J","family":"Jaehnig","sequence":"additional","affiliation":[{"name":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX 77030, USA"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8676-2425","authenticated-orcid":false,"given":"Bing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX 77030, USA"},{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,10,22]]},"reference":[{"key":"2022121418364806400_btac698-B1","doi-asserted-by":"crossref","first-page":"5031","DOI":"10.1016\/j.cell.2021.08.023","article-title":"Proteogenomic characterization of pancreatic ductal adenocarcinoma","volume":"184","author":"Cao","year":"2021","journal-title":"Cell"},{"key":"2022121418364806400_btac698-B2","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.cels.2019.03.010","article-title":"Performance assessment and selection of normalization procedures for single-cell RNA-Seq","volume":"8","author":"Cole","year":"2019","journal-title":"Cell Syst"},{"key":"2022121418364806400_btac698-B3","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol"},{"key":"2022121418364806400_btac698-B4","doi-asserted-by":"crossref","first-page":"19737","DOI":"10.1038\/s41598-020-76881-x","article-title":"Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis","volume":"10","author":"Corchete","year":"2020","journal-title":"Sci. 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