@Article{Gruning_Fallmann_Yusuf-The_RNA_workb-NAR2017,
  author =	 {Gruning, Bjorn A. and Fallmann, Jorg and Yusuf, Dilmurat 
                  and Will, Sebastian and Erxleben, Anika and Eggenhofer, 
                  Florian and Houwaart, Torsten and Batut, Berenice 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},
  volume =	 {45},
  number =	 {W1},
  pages =	 {W560-W566},
  user =	 {backofen},
  pmid =	 {28582575},
  doi = 	 {10.1093/nar/gkx409},
  issn = 	 {1362-4962},
  issn = 	 {0305-1048},
  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.}
}