Related Experiment Video
Updated: Feb 28, 2026

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
Published on: September 18, 2021
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from
Igor Mandric1, Yvette Temate-Tiagueu1, Tatiana Shcheglova2
1Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA.
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.
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