Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data

• DOI: 10.1093/bioinformatics/btx365
• Publication Date: 2017-06-07T03:11:55Z
• Authors: Igor Mandric; Yvette Temate-Tia...; Tatiana Shcheglova; Sahar Al Seesi; Alex Zelikovsky; Ion I Măndoiu
• Keywords: Bootstrapping (finance); Graphical user interface; Interface (matter); Expression (computer science)

This note presents IsoEM2 and IsoDE2, new versions with enhanced features faster runtime of the IsoEM IsoDE packages for expression level estimation differential expression. estimates fragments per kilobase million (FPKM) transcript (TPM) levels genes isoforms confidence intervals through bootstrapping, while IsoDE2 performs analysis using bootstrap samples generated by IsoEM2. Both tools are available a command line interface as well graphical user (GUI) wrappers Galaxy platform.The source code this software suite is at https://github.com/mandricigor/isoem2. The https://toolshed.g2.bx.psu.edu/view/saharlcc/isoem2_isode2/[e-mail] or [e-mail] data Bioinformatics online.