S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.
S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.
It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis (between two conditions, for instance). S-MART also provides many ways to visualize your data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots).

S-MART does not require a computer science background and thus can be used by all biologists through a graphical interface. S-MART can run on any personal computer, yielding results within an hour for most queries.

The tool has been published:
Zytnicki M, Quesneville H (2011) S-MART, A Software Toolbox to Aid RNA-seq Data Analysis. PLoS ONE 6(10): e25988. doi:10.1371/journal.pone.0025988