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Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research

Sophia Clara Mädler, Alice Julien-Laferriere, Luis Wyss, Miroslav Phan, Albert S. W. Kang, Eric Ulrich, Roland Schmucki, Jitao David Zhang, Martin Ebeling, Laura Badi, Tony Kam-Thong, Petra C. Schwalie, Klas Hatje
doi: https://doi.org/10.1101/2020.08.11.245795
Sophia Clara Mädler
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Alice Julien-Laferriere
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
2Soladis GmbH, Basel, Switzerland
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Luis Wyss
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
3Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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Miroslav Phan
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
3Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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Albert S. W. Kang
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Eric Ulrich
4Roche Pharma Research and Early Development, I2O Disease Translational Area, Roche Innovation Center Basel, Basel, Switzerland
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Roland Schmucki
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Jitao David Zhang
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Martin Ebeling
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Laura Badi
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Tony Kam-Thong
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Petra C. Schwalie
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Klas Hatje
1Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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  • For correspondence: klas.hatje@roche.com
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Abstract

Single-cell RNA sequencing (scRNA-seq) revolutionised our understanding of disease biology and presented the promise of transforming translational research. We developed Besca, a toolkit that streamlines scRNA-seq analyses according to current best practices. A standard workflow covers quality control, filtering, and clustering. Two complementary Besca modules, utilizing hierarchical cell signatures or supervised machine learning, automate cell annotation and provide harmonised nomenclatures across studies. Subsequently, Besca enables estimation of cell type proportions in bulk transcriptomics studies. Using multiple heterogeneous scRNA-seq datasets we show how Besca aids acceleration, interoperability, reusability, and interpretability of scRNA-seq data analysis, crucial aspects in translational research and beyond.

Competing Interest Statement

All authors were previously or are currently employed by F. Hoffmann-La Roche Ltd. AJL is employed by Soladis GmbH. The authors declare that they have no other competing interests.

Footnotes

  • https://github.com/bedapub/besca

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted September 01, 2020.
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Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research
Sophia Clara Mädler, Alice Julien-Laferriere, Luis Wyss, Miroslav Phan, Albert S. W. Kang, Eric Ulrich, Roland Schmucki, Jitao David Zhang, Martin Ebeling, Laura Badi, Tony Kam-Thong, Petra C. Schwalie, Klas Hatje
bioRxiv 2020.08.11.245795; doi: https://doi.org/10.1101/2020.08.11.245795
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Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research
Sophia Clara Mädler, Alice Julien-Laferriere, Luis Wyss, Miroslav Phan, Albert S. W. Kang, Eric Ulrich, Roland Schmucki, Jitao David Zhang, Martin Ebeling, Laura Badi, Tony Kam-Thong, Petra C. Schwalie, Klas Hatje
bioRxiv 2020.08.11.245795; doi: https://doi.org/10.1101/2020.08.11.245795

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