STAS-seq: Statistical Analysis Suite for RNA-seq data

Abstract

Summury: We present STAS-seq, an R-based statistical analysis suite for read count data from RNA-seq. Its user-friendly graphic user interface (GUI) provides a workflow that covers data loading, data preprocessing (filtering and normalization), statistical analysis (DEGSeq, edgeR, DESeq, PoissonSeq, and SAMseq), and functional annotation (gene set analysis based on Gene Ontology). Datasets of various experimental designs (unpaired two-class, paired two-class, multiclass, and quantitative) in a simple input format can be analyzed. User-developed plug-in modules for the identification of differentially expressed genes (DEGs) or gene set analysis can be incorporated into STAS-seq.

Availability: STAS-seq is freely available for academic purposes on the Windows and Mac operating systems. Source codes, example data sets and supplementary documentation can be found at http://stas-seq.kobic.re.kr.

Keywords: RNA-seq, R GUI, differentially expressed genes (DEGs), Gene Set analysis