RobiNA, a User Friendly Graphical Interface to Powerful Open Source Microarray and RNA-Seq* Processing
*Please try out the new RNA-Seq analysis workflow included in RobiNA and help us make it more useful by sending us your feedback concerning bugs, missing features etc. Thanks!
THE LATEST VERSION OF ROBINA AT LEAST ON WINDOWS SEEMS TO ERROUNSLY CONCATENATES GZ FILES IN THE ALIGNMENT STEP
We are currently looking into this, until then, please unzip files manually.
Several commercial programs such as GeneSpring featuring a rich and simple user interface to statistically analyze high-throughput "omics" data are available. However, these are usually very expensive and might even require an annual subscription. On the other hand, there are free, open source tools such as BioConductor which offer great statistical options and support for free, but this power often comes at the price of usability, since these tools often feature either only a command line interface or solely very basic user interaction.
Finally, there are tools such as RMA Express which offer a rich user interface but only a very limited set of options.
RobiNA tries to bridge this gap by providing a flexible user friendly graphical interface to unleash the power of R/BioConductor for the individual biologist. RobiNA comes as a convenient all-in-one installation package, that automatically installs the application itself plus all required external tools (i.e. the R and BioConductor frameworks and bowtie).
Currently, using RobiNA it is possible to analyse Illumina/Solexa-based RNA-Seq data (supplied in FASTQ format), Affymetrix data and generic tabular two color or single channel array data.
Furthermore, RobiNA offers a variety of quality control methods that can be used to gain an overview of the experimental data technical quality and structure. Using the built-in graphical experiment designer, researchers can define which samples to compare (even combinations of samples are possible) and finally produce a comprehensive set of tables and plots giving detailed results of the experiment such as the log fold change (M), average expression (A) values at a (user-adjustable) probability for differential expression. Tables summarizing information on the top 100 differentially regulated genes and several plots visualizing the quality of each chip or RNA-Seq library are also generated. The results can directly be imported into MapMan and PageMan for visualization and further analysis.
Please also see the RobiNA quick guide and Robin and RobiNA user's manual which contain step-by-step walkthroughs for the analysis workflows plus further information.
RobiNA was developed for min. Java version 6. If the Java runtime environment is not installed on your system, the installer packages will detect this and direct you to a download source for Java automatically.
A RNA-Seq dataset that can be used for testing RobiNA can be downloaded here. The archive contains:
1) A sample of raw sequence data obtained from the study SRP009936 as deposited in
the European Nucleotide Archive (ENA)
2) The current arabidopsis transcriptome (TAIR10 cds) to be used as the reference in the mapping step.
3) The current arabidopsis genome release (TAIR10_all_chr.fas) plus the corresponding GFF3 annotation file
to be used as reference genome in the mapping step.
For further information, please contact Bjoern Usadel, Marie Bolger.
When using RobiNA (both for microarray and RNA-Seq analysis), please cite:
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. (2012) RobiNA: A
user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7.
Citation for Robin (includes only the microarray analysis workflows):
Lohse M, Nunes-Nesi A, Krueger P, Nagel A, Hannemann J, Giorgi FM, Childs L, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B (2010) Robin: An intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiology, 153:642-51
Download: RobiNA_v1.2.4_build656 Download: RobiNA_v1.2.4_build656
|MacOSX Installer( GNU LGPL v3.0)|
|Windows Installer( GNU LGPL v3.0)|
|Jar File( GNU LGPL v3.0)|
|Windows Installer( GNU LGPL v3.0)|