{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T00:55:44Z","timestamp":1772240144066,"version":"3.50.1"},"posted":{"date-parts":[[2023,2,15]]},"group-title":"Bioinformatics","reference-count":15,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Next generation sequencing technologies enable the analysis of the transcriptomes of individual cells, providing a higher resolution of gene expression and function at the single cell level. Various single-cell data are continuously generated every year, covering fields from scientific research to clinical development. The fast-growing public datasets are collected by distinctive platforms, which are designed to facilitate biological discoveries, disease diagnosis, and new treatments. However, these platforms are hard to meet the urgency of having a unified data integration pipeline to improve comparability between datasets. Here we present SynEcoSys, an online multifunctional platform for single-cell transcriptomic data analysis, visualization, and exploration. SynEcoSys by Singleron Biotechnologies currently provides a massive collection of publicly available single-cell sequencing dataset, involving 46,326,175 cells from 731 datasets across multiple platforms and species. All datasets are generated with a strict and uniform data analysis pipeline and cell marker-based manual annotation, thus facilitating more comprehensive and reliable data mining. SynEcoSys is available at:\n                  <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.synecosys.com\">https:\/\/www.synecosys.com<\/jats:ext-link>\n                  .\n                <\/jats:p>","DOI":"10.1101\/2023.02.14.528566","type":"posted-content","created":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T12:01:17Z","timestamp":1676462477000},"source":"Crossref","is-referenced-by-count":10,"title":["SynEcoSys: a multifunctional platform of large-scale single-cell omics data analysis"],"prefix":"10.64898","author":[{"given":"Yan","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Bingyu","family":"Li","sequence":"additional","affiliation":[]},{"given":"Jiachen","family":"Duan","sequence":"additional","affiliation":[]},{"given":"Xuezhen","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Xiaogang","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Jun","family":"Ye","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Veloso","sequence":"additional","affiliation":[]},{"given":"Jue","family":"Fan","sequence":"additional","affiliation":[]},{"given":"Nan","family":"Fang","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2023021711250961000_2023.02.14.528566v1.1","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1016\/j.csbj.2021.06.043","article-title":"UCell: Robust and scalable single-cell gene signature scoring","volume":"19","year":"2021","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"2023021711250961000_2023.02.14.528566v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/75556"},{"key":"2023021711250961000_2023.02.14.528566v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-0969-x"},{"issue":"9","key":"2023021711250961000_2023.02.14.528566v1.4","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1038\/s41587-021-00896-6","article-title":"Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID","volume":"39","year":"2021","journal-title":"Nature Biotechnology"},{"key":"2023021711250961000_2023.02.14.528566v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00972-2"},{"key":"2023021711250961000_2023.02.14.528566v1.6","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq968"},{"key":"2023021711250961000_2023.02.14.528566v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz1031"},{"issue":"12","key":"2023021711250961000_2023.02.14.528566v1.8","first-page":"12","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","year":"2019","journal-title":"Nature Methods"},{"key":"2023021711250961000_2023.02.14.528566v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa1024"},{"issue":"19","key":"2023021711250961000_2023.02.14.528566v1.10","doi-asserted-by":"crossref","first-page":"1700244","DOI":"10.1002\/pmic.201700244","article-title":"OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets","volume":"17","year":"2017","journal-title":"Proteomics"},{"key":"2023021711250961000_2023.02.14.528566v1.11","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1032"},{"key":"2023021711250961000_2023.02.14.528566v1.12","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0"},{"issue":"4","key":"2023021711250961000_2023.02.14.528566v1.13","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data","volume":"8","year":"2019","journal-title":"Cell Systems"},{"issue":"3","key":"2023021711250961000_2023.02.14.528566v1.14","first-page":"100141","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","year":"2021","journal-title":"Innovation (Cambridge (Mass.))"},{"key":"2023021711250961000_2023.02.14.528566v1.15","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-1950-6"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.02.14.528566","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:16:32Z","timestamp":1768450592000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.02.14.528566"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,15]]},"references-count":15,"URL":"https:\/\/doi.org\/10.1101\/2023.02.14.528566","relation":{},"subject":[],"published":{"date-parts":[[2023,2,15]]},"subtype":"preprint"}}