LOgo SBI Uni Rostock

SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
  +49 381 498-7571
  olaf.wolkenhauer@uni-rostock.de

de.STAIR: Structured Analysis and Integration of RNA-Seq Experiments

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.

We provide these services as part of the German Network for Bioinformatics Infrastructure (de.NBI), which is the German node of ELIXIR. Here, we:

  • 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.

 

Training courses

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
September 2018 Osnabrück
 RNA-Seq data analysis with Galaxy for clinical applications
March 2019 Rostock Galaxy for linking bisulfite sequencing with RNA sequencing
September 2019 Dortmund RNA-Seq data analysis with Galaxy for clinical applications
October Freiburg Galaxy for linking bisulfite sequencing with RNA sequencing

 

Contacts

de.STAIR

Twitter: @denbi_deSTAIR

Contribute: Github

 

Funding

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:

http://destair.bioinf.uni-leipzig.de/

Related publications

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples​

Uellendahl-Werth F, Wolfien M, Franke A, Wolkenhauer O, Ellinghaus D

Scientific Reports 2020, 10, 5630

DOI: https://doi.org/10.1038/s41598-020-62637-0

URL: https://www.nature.com/articles/s41598-020-62637-0?proof=true

Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression

Mucha S, ... Bej S, ..., Wolfien M, ..., Wolkenhauer O, ..., Ellinghaus D

The Journal of Allergy and Clinical Immunology 2019

DOI: https://doi.org/10.1016/j.jaci.2019.10.030

URL: https://www.sciencedirect.com/science/article/abs/pii/S0091674919314800

The RNA workbench 2.0: next generation RNA data analysis

Fallmann J, Pavankumar V, Bagnacani A, ..., Gruening BA

Nucleic Acid Research

DOI: https://doi.org/10.1093/nar/gkz353

Community-driven data analysis training for biology

Batut B, Hiltemann S, Bagnacani A, …, Wolfien M, ..., Gruening B

Cell Systems 2018

DOI: https://doi.org/10.1016/j.cels.2018.05.012

URL: https://www.sciencedirect.com/science/article/pii/S2405471218302308

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

DOI: https://doi.org/10.1007/s41019-017-0050-4

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

DOI: https://doi.org/10.1016/j.jbiotec.2017.06.1203

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

DOI: https://doi.org/10.1093/nar/gkx409

Single-Cell RNA Sequencing Procedures and Data Analysis

Wolfien M, David R, Galow AM

Exon Publications, Brisbane, Australia (2021), chapter in Bioinformatics.

ISBN 13 (online): 978-0-6450017-1-6

DOI: https://doi.org/10.36255/exonpublications.bioinformatics.2021.ch2

URL: https://exonpublications.com/index.php/exon/article/view/265

Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis

Bagnacani A, Wolfien M, Wolkenhauer O

Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.

DOI: https://doi.org/10.1007/978-1-4939-8982-9_8

Workflow Development for the Functional Characterization of ncRNAs

Wolfien M, Brauer DL, Bagnacani A, Wolkenhauer O

Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.

DOI: https://doi.org/10.1007/978-1-4939-8982-9_5

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