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TS has been associated with human diseases, plant development and stress responses. Its investigation is often hampered by a lack of suitable tools allowing comprehensive and flexible TS analysis for high-throughput RNA sequencing (RNA-Seq) data. Here, we present deepTS, a user-friendly web-based implementation that enables a fully interactive, multifunctional identification, visualization and analysis of TS events for large-scale RNA-Seq datasets from pairwise, temporal and population experiments. deepTS offers rich functionality to streamline RNA-Seq-based TS analysis for both model and non-model organisms and for those with or without reference transcriptome. The presented case studies highlight the capabilities of deepTS and demonstrate its potential for the transcriptome-wide TS analysis of pairwise, temporal and population RNA-Seq data. We believe deepTS will help research groups, regardless of their informatics expertise, perform accessible, reproducible and collaborative TS analyses of large-scale RNA-Seq data.<\/jats:p>","DOI":"10.1093\/bib\/bbaa137","type":"journal-article","created":{"date-parts":[[2020,6,8]],"date-time":"2020-06-08T11:08:51Z","timestamp":1591614531000},"source":"Crossref","is-referenced-by-count":5,"title":["Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS"],"prefix":"10.1093","volume":"22","author":[{"given":"Zhixu","family":"Qiu","sequence":"first","affiliation":[{"name":"Ma\u2019s Lab"}]},{"given":"Siyuan","family":"Chen","sequence":"additional","affiliation":[{"name":"Ma\u2019s Lab"}]},{"given":"Yuhong","family":"Qi","sequence":"additional","affiliation":[{"name":"Ma\u2019s Lab"}]},{"given":"Chunni","family":"Liu","sequence":"additional","affiliation":[{"name":"Ma\u2019s 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