S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.

Presentation

Several tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have developed a toolbox, S-MART, which handles mapped RNA-Seq and ChIP-Seq 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
• It is registered at the Agency for the Protection of Programs under the deposit number IDDN.FR.001.120025.000.R.C.2012.000.31235

You like S-MART?

 If you are interested in using S-MART, if you wish other tools in the toolbox, or if you want to contribute, please feel free to contact me .

Implementation and Availability

S-MART is implemented in Python for the algorithms and Java for the GUI. S-MART has been tested on Linux, MS Windows and Mac.

Get the documentation .

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