AltAnalyze is an analysis tool designed to analyze your RNA-Seq aligned sequences or Affymetrix CEL files to produce annotated gene expression files with group statistics and alternative exon analysis results, along with a wide array of functional enrichment and data visualization outputs. AltAnalyze can be used for conventional microarrays (gene expression only), RNASeq data, as well as splicing sensitive arrays (exon and junction). This software performs identical analyses on both Affymetrix Gene 1.0 and Exon 1.0 arrays. In addition to Affymetrix CEL file analyses, AltAnalyze can perform gene expression analyses on post-normalized expression files for array manufacturers with annotations at Ensembl (e.g., Illumina, Agilent).

A comprehensive documentation page is available on Read The Docs.

Alternative Exon Analyses

With AltAnalyze and the integrated software DomainGraph (Cytoscape), users have access to a wide spectrum of predictions on the impact of alternative exon inclusion on protein sequence, domain sequence and microRNA binding site inclusion. Specific features include:

  • Identification and visualization of associated protein isoforms
  • Identification and visualization of affected protein domains/motifs
  • Pathway over-representation and visualization
  • Domain/motif over-representation

For more information, see our AboutUs page.