The IsoEM package can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. IsoEM uses an Expectation-Maximization (EM) algorithm based on a probabilistic model that takes into account the fragment length distribution, with mean/standard deviations specified by the user or automatically inferred when using paired-end reads. The current version (IsoEM2) generates bootstrap-based confidence intervals for the TPM/FPKM estimates and is distributed along with the IsoDE2 package for performing bootstrap-based differential expression analysis. For details see our Bioinformatics Application Note.

Source code and sample data

The IsoEM2/IsoDE2 software is written in Java so it can be run on any platform with a Java virtual machine. See the README file for installation instructions. Wrappers for the Galaxy platform along with a sample dataset and instructions for testing the installation of IsoEM2 and IsoDE2 are also included below.

NEW! Public Galaxy installation

A public Galaxy deployment of IsoEM2 is now available at

Contact Information

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Acknowledgment and Disclaimer

This material is based upon work supported in part by awards CCF-16119110, CCF-1618347, DBI-1564936, DBI-1564899, IIS-0916948, IIS-0916401, and IIS-0546457 from the National Science Foundation, a Collaborative Research Grant from Life Technologies, and a Molecular Basis of Disease Fellowship from Georgia State University. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.