MeV

Built in Java, MeV is an advanced software application designed for genomic data exploration, enabling you to seamlessly analyze microarray gene expressions.

As long as you have Java installed on your  PC, you don't need to set up anything else. This means that you can drop the program files anywhere on the disk and directly launch MeV.

It's also possible to save it to a pen drive to quickly run it on any  PC with minimum effort. Unlike most installers, it doesn't add new entries to the Windows registry.

At startup, MeV asks for permission to connect to the Internet, in order to enhance its functionality. It's wrapped in a user-friendly interface, which consists of two graphical windows (multiple array and experiment viewers), along with a command-line dialog.

Files with expression data can be loaded from tab-delimited multiple samples with single or two-color arrays. Annotations can be optionally included, and you can also choose the organism and array. After MeV downloads the necessary data, you can study the expression table and apply it to your project.

In the main app window it's possible to analyze the original data and results, manage clusters and scripts, as well as to review history. MeV lets you adjust data, change the metrics system, save the matrix or image, append gene or sample annotations, rename the species, and so on.

The tool didn't put a strain on the overall performance of the computer in our testing, thanks to the fact that it needed low CPU and RAM to work properly. On the other hand, it hasn't been updated for a pretty long time, and its interface could definitely use some improvements. Otherwise, you can test MeV for yourself, since it's freeware.