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Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.<\/jats:p>","DOI":"10.1093\/bib\/bbaa001","type":"journal-article","created":{"date-parts":[[2020,1,2]],"date-time":"2020-01-02T12:07:51Z","timestamp":1577966871000},"page":"1706-1728","source":"Crossref","is-referenced-by-count":336,"title":["The bioinformatics toolbox for circRNA discovery and analysis"],"prefix":"10.1093","volume":"22","author":[{"given":"Liang","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Computer Science, Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University"}]},{"given":"Changliang","family":"Wang","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, University of Macau"}]},{"given":"Huiyan","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence, Jilin 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