AltAnalyze is an easy-to-use application for the end-to-end analysis of single-cell (ICGS) and bulk RNA-Seq data. For splicing sensitive platforms (single cell/bulk RNA-Seq or microarrays), 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 and examples in our interactive browsers.
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 splicing events can be visualized
in the context of proteins, domains, microRNA
binding sites and using SashimiPlots in this software.
For program details and to get answers
to common questions, check out our Manual, Sample Data, Wiki, FAQ, Tutorials or User Group.