SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
de.STAIR: Structured Analysis and Integration of RNA-Seq Experiments
RNA Sequencing (RNA-Seq) has become a widely used tool to study quantitative and qualitative aspects of the transcriptome. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. We provide easy access to comprehensive analysis of RNA-Seq experiments as a service. To do so, we leverage on the Galaxy framework, and organise dedicated workshops, training programs, and screencasts to make Life Scientists familiar with computational approaches to biological problems.
- Build flexible workflows for RNA-Seq protocols and experimental designs
- Integrate novel analysis methods with the RNA Bioinformatics Center (RBC) workbench
These new workflows and tools will become integral parts of RBC's Galaxy instance, to ensure portability of tools, workflows and pipelines, ultimately facilitating reproducibility. To make users confident with the Galaxy platform, we take part in the de.NBI training program, and contribute to the Galaxy training material. Finally, we provide video tutorials for introducing the Galaxy platform.
We are available for on-site training courses, to cover diverse aspects of RNA-Seq topics, such as data pre-processing, mapping, and visualisation of differential gene expression analyses. Contact us!
|October 2016||Berlin||Using NGS Data Analysis in the Clinic|
|December 2016||Porto||Genomic Applications in Biotechnology|
|March 2017||Ljubljana||Customized Sequencing Data Analysis with Galaxy|
|September 2017||Oldenburg||Introduction to RNA-Seq Data Analysis with Galaxy|
|October 2017||Freiburg||A Primer for RNA-Seq Processing, Interpreting and Visualization|
|March 2018||Kiel||Introduction to RNA-Seq Data Analysis with Galaxy|
|June 2018||Jena||A Primer for RNA-Seq Processing, Interpretation and Visualization|
||RNA-Seq data analysis with Galaxy for clinical applications|
|March 2019||Rostock||Galaxy for linking bisulfite sequencing with RNA sequencing|
This project is funded by the German Federal Ministry for Education and Research (BMBF) program de.NBI-Partner (Grant 031L0106).
Visit our official Project-Website:
Community-driven data analysis training for biology
Batut B, Hiltemann S, Bagnacani A, …, Wolfien M, ..., Gruening B
Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis
Möller S, ..., Bagnacani A, ..., Crusoe MR
Springer Data Science and Engineering
Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments
Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR
Journal of Biotechnology
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
Gruening BA, ..., Bagnacani A, Wolfien M, ..., Wolkenhauer O, ..., Backofen R
Nucleic Acids Research