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).

 


News
: August 31, 2016. A new 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 microarry, single-cell (ICGS) and bulk RNA-Seq data. For splicing sensitive platforms (single cell/bulk RNA-Seq or Affymetrix Exon, Gene and Junction arrays), 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. Updates 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 the Manual, Wiki, FAQ, Tutorials or User Group.

 
Downloads

Release version 2.1.0 - 8/31/16
 
- Mac OSX Installer (.dmg)  
- Windows Archive (.zip)    
- Ubuntu Archives (.zip) 32bit 64bit    
- Cross Platform (.zip)    
  archived versions    

Documentation
 
null Manual and Installation Guide
null Tutorials
null News and Updates
null How to Cite
null Contact Us
null AboutUs
null Blog
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