Downloaded over 10,000 times and cited in over 100 peer-reviewed publications. AltAnalyze has hundreds of active users and is being actively developed as an open-source project.

AltAnalyze recieves funding from the NHLBI Progenitor Cell Biology Consortium (U01HL099997).


AltAnalyze - Comprehensive Transcriptome Analysis

AltAnalyze is an easy-to-use application for the end-to-end analysis of microarry, RNA-Seq and metabolomics data. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will 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). Specialized methods exist for the automatic identification of coherent single-cell populations (gene expression and alternative splicing).

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 the Manual, Wiki, FAQ, Tutorials or User Group.


Release version - 4/06/16
- Mac OSX Installer (.dmg)  
- Windows Archive (.zip)    
- Ubuntu Archives (.zip) 32bit 64bit    
- Cross Platform (.zip)    
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