Downloaded over 17,000 times and cited in over 200 peer-reviewed publications. AltAnalyze has hundreds of active users and is being actively developed as an open-source project.

AltAnalyze recieves funding from NIH National Cancer Institute (R01CA226802).

 


News
: A new manuscript describing the cellHarmony workflow in AltAnlayze and its application to the Human Cell Atlas is described here.

 

 

 

 
AltAnalyze - Comprehensive Transcriptome Analysis

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.