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

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A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
GigaScience ( IF 9.2 ) Pub Date : 2020-10-20 , DOI: 10.1093/gigascience/giaa102
Mehmet Tekman ₁ , Bérénice Batut ₁ , Alexander Ostrovsky ₂ , Christophe Antoniewski _{3,

4} , Dave Clements ₂ , Fidel Ramirez ₅ , Graham J Etherington ₆ , Hans-Rudolf Hotz _{7,

8} , Jelle Scholtalbers ₉ , Jonathan R Manning ₁₀ , Lea Bellenger ₃ , Maria A Doyle _{11,

12} , Mohammad Heydarian ₂ , Ni Huang _{10,

13} , Nicola Soranzo ₆ , Pablo Moreno ₁₀ , Stefan Mautner ₁ , Irene Papatheodorou ₁₀ , Anton Nekrutenko ₁₄ , James Taylor ₂ , Daniel Blankenberg ₁₅ , Rolf Backofen ₁ , Björn Grüning ₁

Affiliation

Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
Department of Biology, Johns Hopkins University, Mudd Hall 144, 3400 N. Charles Street, Baltimore, MD 21218, USA.
ARTbio, Sorbonne Université, CNRS FR 3631, Inserm US 037, Paris, France.
Institut de Biologie Paris Seine, 9 Quai Saint-Bernard Université Pierre et Marie Curie, Campus Jussieu, Bâtiments A-B-C, 75005 Paris, France.
Boehringer Ingelheim International GmbH, Binger Strasse 173, 55216 Ingelheim am Rhein, Biberach, Germany.
Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
SIB Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland.
European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
Research Computing Facility, Peter MacCallum Cancer Centre, Melbourne, 305 Grattan Street, Victoria 3000, Australia.
Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia.
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NB21 Cleveland, OH 44195, USA.

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.

中文翻译：

使用 Galaxy 框架的单细胞 RNA 测序训练和分析套件

直到最近，庞大的单细胞 RNA 测序工具生态系统一直受到过多的不同分析策略、不一致的文件格式以及不同软件套件之间的兼容性问题的困扰。10x Genomics 数据集的采用已经开始平息这种多样性，生物信息学社区再次倾向于处理和理解这些不断增长的数据集所需的大型计算需求和统计驱动方法。

更新日期：2020-10-20

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