AltAnalyze is an easy-to-use application for microarry, RNA-Seq and metabolomics analysis. 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. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (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.
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 with the Cytoscape Plugin DomainGraph.
For program details and to get answers
to common questions, check out the Manual, Wiki, FAQ, Tutorials or User Group.