@article{Gruning_Fallmann_Yusuf-The_RNA_workb-NAR2017,
author = {Grüning, Björn A. and Fallmann, Jörg and Yusuf, Dilmurat 
          and Will, Sebastian and Erxleben, Anika and Eggenhofer, 
          Florian and Houwaart, Torsten and Batut, Bérénice and Videm, 
          Pavankumar and Bagnacani, Andrea and Wolfien, Markus and 
          Lott, Steffen C. and Hoogstrate, Youri and Hess, Wolfgang R. 
          and Wolkenhauer, Olaf and Hoffmann, Steve and Akalin, Altuna 
          and Ohler, Uwe and Stadler, Peter F. and Backofen, Rolf},
title = {The {RNA} workbench: best practices for {RNA} and 
         high-throughput sequencing bioinformatics in {Galaxy}},
journal = {NAR},
year = {2017},
doi = {10.1093/nar/gkx409},
volume = {45},
user = {backofen},
pmid = {28582575},
pages = {W560-W566},
number = {W1},
issn = {1362-4962},
abstract = {RNA-based regulation has become a major research topic in 
            molecular biology. The analysis of epigenetic and expression 
            data is therefore incomplete if RNA-based regulation is not 
            taken into account. Thus, it is increasingly important but 
            not yet standard to combine RNA-centric data and analysis 
            tools with other types of experimental data such as RNA-seq 
            or ChIP-seq. Here, we present the RNA workbench, a 
            comprehensive set of analysis tools and consolidated 
            workflows that enable the researcher to combine these two 
            worlds. Based on the Galaxy framework the workbench 
            guarantees simple access, easy extension, flexible adaption 
            to personal and security needs, and sophisticated analyses 
            that are independent of command-line knowledge. Currently, 
            it includes more than 50 bioinformatics tools that are 
            dedicated to different research areas of RNA biology 
            including RNA structure analysis, RNA alignment, RNA 
            annotation, RNA-protein interaction, ribosome profiling, 
            RNA-seq analysis and RNA target prediction. The workbench is 
            developed and maintained by experts in RNA bioinformatics 
            and the Galaxy framework. Together with the growing 
            community evolving around this workbench, we are committed 
            to keep the workbench up-to-date for future standards and 
            needs, providing researchers with a reliable and robust 
            framework for RNA data analysis. AVAILABILITY: The RNA 
            workbench is available at 
            https://github.com/bgruening/galaxy-rna-workbench.}
}