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We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g.\u00a0miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https:\/\/www.ccb.uni-saarland.de\/mirmaster2.<\/jats:p>","DOI":"10.1093\/nar\/gkab268","type":"journal-article","created":{"date-parts":[[2021,4,16]],"date-time":"2021-04-16T21:01:58Z","timestamp":1618606918000},"page":"W397-W408","source":"Crossref","is-referenced-by-count":50,"title":["miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1967-2918","authenticated-orcid":false,"given":"Tobias","family":"Fehlmann","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8223-3750","authenticated-orcid":false,"given":"Fabian","family":"Kern","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}]},{"given":"Omar","family":"Laham","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9330-9290","authenticated-orcid":false,"given":"Christina","family":"Backes","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}]},{"given":"Jeffrey","family":"Solomon","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}]},{"given":"Pascal","family":"Hirsch","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}]},{"given":"Carsten","family":"Volz","sequence":"additional","affiliation":[{"name":"Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbr\u00fccken, Germany"}]},{"given":"Rolf","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5361-0895","authenticated-orcid":false,"given":"Andreas","family":"Keller","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"},{"name":"Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,4,19]]},"reference":[{"key":"2021070812000935800_B1","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cell.2018.03.006","article-title":"Metazoan microRNAs","volume":"173","author":"Bartel","year":"2018","journal-title":"Cell"},{"key":"2021070812000935800_B2","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.3390\/cells8111465","article-title":"The non-canonical aspects of microRNAs: many roads to gene regulation","volume":"8","author":"Stavast","year":"2019","journal-title":"Cells"},{"key":"2021070812000935800_B3","doi-asserted-by":"crossref","first-page":"8731","DOI":"10.1093\/nar\/gkx595","article-title":"Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs","volume":"45","author":"Fehlmann","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021070812000935800_B4","doi-asserted-by":"crossref","first-page":"3771","DOI":"10.18632\/oncotarget.14054","article-title":"Exploring ncRNAs in Alzheimer's disease by miRMaster","volume":"8","author":"Fehlmann","year":"2017","journal-title":"Oncotarget"},{"key":"2021070812000935800_B5","doi-asserted-by":"crossref","first-page":"1836","DOI":"10.1093\/bib\/bby054","article-title":"Trends in the development of miRNA bioinformatics tools","volume":"20","author":"Chen","year":"2019","journal-title":"Brief. 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