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

Igor Mandric | Zendy; Yvette TemateTiagueu | Zendy; Tatiana Shcheglova | Zendy; Sahar Al Seesi | Zendy; Alex Zelikovsky | Zendy; Ion Măndoiu | Zendy

Open Access

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

Author(s) -

Igor Mandric,

Yvette TemateTiagueu,

Tatiana Shcheglova,

Sahar Al Seesi,

Alex Zelikovsky,

Ion Măndoiu

Publication year - 2017

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btx365

Subject(s) - bootstrapping (finance) , computer science , software , source code , graphical user interface , interface (matter) , expression (computer science) , differential (mechanical device) , confidence interval , data mining , operating system , programming language , statistics , mathematics , bubble , maximum bubble pressure method , engineering , econometrics , aerospace engineering

This note presents IsoEM2 and IsoDE2, new versions with enhanced features and faster runtime of the IsoEM and IsoDE packages for expression level estimation and differential expression. IsoEM2 estimates fragments per kilobase million (FPKM) and transcript per million (TPM) levels for genes and isoforms with confidence intervals through bootstrapping, while IsoDE2 performs differential expression analysis using the bootstrap samples generated by IsoEM2. Both tools are available with a command line interface as well as a graphical user interface (GUI) through wrappers for the Galaxy platform.

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