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Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at the Ohio State University, we have applied the pipeline to a few publicly available RNAseq datasets downloaded from GEO in order to demonstrate the feasibility of this workflow. Source code is available here: workflow: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/code.bmi.osumc.edu\/gadepalli.3\/BISR-RNAseq-ICIBM2019\">https:\/\/code.bmi.osumc.edu\/gadepalli.3\/BISR-RNAseq-ICIBM2019<\/jats:ext-link> and shiny: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/code.bmi.osumc.edu\/gadepalli.3\/BISR_RNASeq_ICIBM19\">https:\/\/code.bmi.osumc.edu\/gadepalli.3\/BISR_RNASeq_ICIBM19<\/jats:ext-link>. Example dataset is demonstrated here: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/dataportal.bmi.osumc.edu\/RNA_Seq\/\">https:\/\/dataportal.bmi.osumc.edu\/RNA_Seq\/<\/jats:ext-link>.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>The workflow allows for the analysis (alignment, QC, gene-wise counts generation) of raw RNAseq data and seamless integration of quality analysis and differential expression results into a configurable R shiny web application.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-019-3251-1","type":"journal-article","created":{"date-parts":[[2019,12,20]],"date-time":"2019-12-20T08:05:23Z","timestamp":1576829123000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation"],"prefix":"10.1186","volume":"20","author":[{"given":"Venkat Sundar","family":"Gadepalli","sequence":"first","affiliation":[]},{"given":"Hatice Gulcin","family":"Ozer","sequence":"additional","affiliation":[]},{"given":"Ayse Selen","family":"Yilmaz","sequence":"additional","affiliation":[]},{"given":"Maciej","family":"Pietrzak","sequence":"additional","affiliation":[]},{"given":"Amy","family":"Webb","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,12,20]]},"reference":[{"key":"3251_CR1","volume-title":"R: the R project for statistical computing","author":"R Core Team","year":"2018","unstructured":"R Core Team. 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