Downloaded over 17,000 times and cited in over 200 peer-reviewed publications. AltAnalyze has hundreds of active users and is being actively developed as an open-source project.

AltAnalyze recieves funding from NIH National Cancer Institute (R01CA226802).


: A manuscript describing the ICGS workflow in AltAnlayze is now online at Nature. See our blog for more information.




AltAnalyze - Comprehensive Transcriptome Analysis

AltAnalyze is an easy-to-use application for the end-to-end analysis of single-cell (ICGS) and bulk RNA-Seq data. For splicing sensitive platforms (single cell/bulk RNA-Seq or microarrays), AltAnalyze can assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. AltAnalyze automates every step of gene expression and splicing analysis other data (FASTQ processing, RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). Easy to follow video tutorials can be found here. New developments can be found on our blog.

AltAnalyze can be run through an inutitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites in the new AltAnalyze Isoform Viewer. For program details and to get answers to common questions, check out our Manual, Sample Data, Wiki, FAQ, Tutorials or User Group.