AltAnalyze is an open source and cross-platform utility that will allow you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting.
AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as well as many conventional array-types (e.g., Illumina, Agilent, Affymetrix).
AltAnalyze can be used either as a command-line or as a graphical user interface based app, and it 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.
What's New in This Release: [ read full changelog ]
· moderated t-tests based based on the limma method,
· analysis of cell composition with the new program LineageProflier,
· robust quality control analysis and visualization,
· hierarchical and principal component analysis clustering/visualization,
· WikiPathways visualization,
· Additional Analyses menu added for streamlined access to visualization and pathway enrichment methods,
· bug fixes to 2.0.6 and
· more sensitive default RNA-Seq expression filtering options.