{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T12:01:43Z","timestamp":1781784103643,"version":"3.54.5"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,2]],"date-time":"2022-12-02T00:00:00Z","timestamp":1669939200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2018YFD0901201"],"award-info":[{"award-number":["2018YFD0901201"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFD1200804"],"award-info":[{"award-number":["2021YFD1200804"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDA24010206"],"award-info":[{"award-number":["XDA24010206"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>With the continuous development of high-throughput sequencing technology, bioinformatic analysis of omics data plays an increasingly important role in life science research. Many R packages are widely used for omics analysis, such as DESeq2, clusterProfiler and STRINGdb. And some online tools based on them have been developed to free bench scientists from programming with these R packages. However, the charts generated by these tools are usually in a fixed, non-editable format and often fail to clearly demonstrate the details the researchers intend to express. To address these issues, we have created Visual Omics, an online tool for omics data analysis and scientific chart editing. Visual Omics integrates multiple omics analyses which include differential expression analysis, enrichment analysis, protein domain prediction and protein\u2013protein interaction analysis with extensive graph presentations. It can also independently plot and customize basic charts that are involved in omics analysis, such as various PCA\/PCoA plots, bar plots, box plots, heat maps, set intersection diagrams, bubble charts and volcano plots. A distinguishing feature of Visual Omics is that it allows users to perform one-stop omics data analyses without programming, iteratively explore the form and layout of graphs online and fine-tune parameters to generate charts that meet publication requirements.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Visual Omics can be used at http:\/\/bioinfo.ihb.ac.cn\/visomics. Source code can be downloaded at http:\/\/bioinfo.ihb.ac.cn\/software\/visomics\/visomics-1.1.tar.gz.<\/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\/btac777","type":"journal-article","created":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T16:12:09Z","timestamp":1669911129000},"source":"Crossref","is-referenced-by-count":12,"title":["Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities"],"prefix":"10.1093","volume":"39","author":[{"given":"Heng","family":"Li","sequence":"first","affiliation":[{"name":"Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mijuan","family":"Shi","sequence":"additional","affiliation":[{"name":"Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China"},{"name":"The Innovative Academy of Seed Design, Chinese Academy of Sciences , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keyi","family":"Ren","sequence":"additional","affiliation":[{"name":"College of Fisheries and Life Science, Dalian Ocean University , Dalian 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weidong","family":"Ye","sequence":"additional","affiliation":[{"name":"Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanting","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China"},{"name":"The Innovative Academy of Seed Design, Chinese Academy of Sciences , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingyin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China"},{"name":"The Innovative Academy of Seed Design, Chinese Academy of Sciences , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8034-1096","authenticated-orcid":false,"given":"Xiao-Qin","family":"Xia","sequence":"additional","affiliation":[{"name":"Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"The Innovative Academy of Seed Design, Chinese Academy of Sciences , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,2]]},"reference":[{"key":"2023010805365140800_btac777-B1","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023010805365140800_btac777-B2","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.1002\/imt2.5","article-title":"ImageGP: an easy-to-use data visualization web server for scientific researchers","volume":"1","author":"Chen","year":"2022","journal-title":"iMeta"},{"key":"2023010805365140800_btac777-B3","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. 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