RobiNA
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Application data |
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| Created by | Lohse MA, Bolger T, Usadel B |
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| Biological application domain(s) | RNA-Seq |
| Principal bioinformatics method(s) | Differentially expressed gene identification |
| Technology | Illumina |
| Created at | Max Planck Institute of Molecular Plant Physiology |
| Maintained? | Yes |
| Input format(s) | Fastq |
| Software features | Trimming, differential expression, graphical display |
| Programming language(s) | Java, R |
| Licence | GPL |
| Operating system(s) | Windows, Linux, Mac OS X |
Summary: RobiNA is a Java GUI that enables the user to graphically call differentially expressed genes. For read mapping it relies on bowtie and for the differntial expression analysis it builds on an R backbone running DESeq and edgeR.
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Description
RobiNA a user-friendly software solution for the analysis of differential gene expression based on next generation RNA-Seq data, building on the Robin tool for microarray analysis and the latest R/Bioconductor packages for RNA-Seq analysis (specifically DESeq and edgeR). The application provides all components for the statistical analysis of RNA Seq data starting with raw sequence data quality assessment, filtering and trimming (using Trimmomatic) of low quality data, mapping of the reads to a reference genome or transcriptome and finally statistical assessment of differential gene expression. Users are guided through each step through a wizard based graphical user interface which was designed based on the experience and feedback from Robin. The interface provides online help for each step.
The results of both the quality assessment and the statistical analysis can be browsed from within the application. However they are also stored in form of a project folder that contains all relevant data, so it can later be assessed and rechecked.
Internally, RobiNA stands on the shoulder of giants by employing the R statistics software where it calls differential expression using the libraries egdeR and DESeq. Furthermore it uses the Bowtie aligner for mapping the reads to a reference sequence. RobiNA was implemented as complete, hassle-free multi platform installation.
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