S-MART
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Application data |
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| Created by | Matthias Zytnicki |
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| Biological application domain(s) | RNA-Seq, ChIP-seq |
| Created at | INRA Versailles |
| Maintained? | Yes |
| Input format(s) | PSL, MAQ, SOAP, SEQMAP, FASTA, FASTQ |
| Output format(s) | TXT, GFF3 |
| Programming language(s) | Python, Java |
| Operating system(s) | Linux, Mac OS X, Windows |
Summary: S-MART manages your RNA-Seq and ChIP-seq data.
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Description
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.
Links
References
To add a reference for S-MART, enter the PubMed ID in the field below and click 'Add'.
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| Web Search | Wiki Sites | Scientific |
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