ArrayStudio is a GUI software in Windows. OmicSoft also provides a command line tool (named Oshell). Oshell.exe is a .NET application, and it has also been optimized in the Linux environment using the MONO application. In this article, I will describe a complete OmicScript pipeline for RNA-Seq data analysis.
OmicSoft is available at http://www.arrayserver.com/wiki/index.php?title=OmicScript_pipeline_for_RNA-Seq_data_analysis