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

Igor Mandric; Yvette Temate-Tiagueu; Tatiana Shcheglova; Sahar Al Seesi; Alex Zelikovsky; Ion I Mandoiu

doi:10.1093/bioinformatics/btx365

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

Bioinformatics. 2017 Oct 15;33(20):3302-3304. doi: 10.1093/bioinformatics/btx365.

Authors

Igor Mandric¹, Yvette Temate-Tiagueu¹, Tatiana Shcheglova², Sahar Al Seesi^{2

3}, Alex Zelikovsky¹, Ion I Mandoiu³

Affiliations

¹ Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA.
² Immunology Department, University of Connecticut Health Center, Farmington, CT 06030, USA.
³ Computer Science and Engineering Department, University of Connecticut, Storrs, CT 06269, USA.

PMID: 28605502
DOI: 10.1093/bioinformatics/btx365

Abstract

Summary: 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.

Availability and implementation: The source code of this software suite is available at https://github.com/mandricigor/isoem2. The Galaxy wrappers are available at https://toolshed.g2.bx.psu.edu/view/saharlcc/isoem2_isode2/.

Contact: imandric1@student.gsu.edu or ion@engr.uconn.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Computational Biology / methods*
Confidence Intervals*
Gene Expression Profiling / methods*
Sequence Analysis, RNA / methods*
Software*