Journal article

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Mehmet Tekman, Berenice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramirez, Graham J Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan R Manning, Lea Bellenger, Maria A Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor Show all

GigaScience | OXFORD UNIV PRESS | Published : 2020

Abstract

BACKGROUND: The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets. RESULTS: Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning exp..

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Grants

Awarded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)


Awarded by Germany's Excellence Strategy (CIBSS EXC-2189)


Awarded by BBSRC


Awarded by Earlham Institute


Awarded by National Institutes of Health


Awarded by Collaborative Research Centre 992 Medical Epigenetics (DFG)


Awarded by German Federal Ministry of Education and Research (BMBF)


Funding Acknowledgements

This project was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) 22977937/GRK2344 and BA2168/3-3, Germany's Excellence Strategy (CIBSS EXC-2189 -Project ID 390939984), the BBSRC Core Strategic Programme Grants BBS/E/T/000PR9814, BBS/E/T/000PR9817, BBS/E/T/000PR9818, and BBS/E/T/000PR9819, Core Capability Grant BBS/E/T/000PR9816 at the Earlham Institute, and the National Institutes of Health grant U41HG006620.The European Galaxy project is in part funded by Collaborative Research Centre 992 Medical Epigenetics (DFG grant SFB 992/1 2012) and German Federal Ministry of Education and Research (BMBF grants 031 A538A/A538C RBC, 031L0101B/031L0101C de.NBI-epi). The article processing charge was funded by the Baden-Wu<spacing diaeresis> rttemberg Ministry of Science, Research and Art and the University of Freiburg in the funding programme Open Access Publishing.