CLC Main Workbench (64-bit)

From CLC bio:

CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.

Features include support for both microarray- and sequencing-based (post-mapping RNA-Seq) expression data, visualization: interactive heat map and scatter plots. Quality control tools including principal component analysis, MA- and box plots. It has ability to import NetAffx annotation arrays and adding annotation to experiments. It also includes transformation and normalization tools.