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.