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scMontage: Fast and Robust Gene Expression Similarity Search for Massive Single-cell Data

Tomoya Mori, Naila Shinwari, View ORCID ProfileWataru Fujibuchi
doi: https://doi.org/10.1101/2020.08.30.271395
Tomoya Mori
1Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Sho-goin, Sakyo-ku, Kyoto 606-8507, Japan
#Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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Naila Shinwari
1Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Sho-goin, Sakyo-ku, Kyoto 606-8507, Japan
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Wataru Fujibuchi
1Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Sho-goin, Sakyo-ku, Kyoto 606-8507, Japan
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  • ORCID record for Wataru Fujibuchi
  • For correspondence: fujibuchi-g@cira.kyoto-u.ac.jp
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Abstract

Single-cell RNA-seq (scRNA-seq) analysis is widely used to characterize cell types or detect heterogeneity of cell states at much higher resolutions than ever before. Here we introduce scMontage (https://scmontage.stemcellinformatics.org), a gene expression similarity search server dedicated to scRNA-seq data, which can rapidly compare a query with thousands of samples within a few seconds. The scMontage search is based on Spearman’s rank correlation coefficient and its robustness is ensured by introducing Fisher’s Z-transformation and Z-test. Furthermore, search results are linked to a human cell database SHOGoiN (http://shogoin.stemcellinformatics.org), which enable users to fast access to additional cell-type specific information. The scMontage is available not only as a web server but also as a stand-alone application for user’s own data, and thus it enhances the reliability and throughput of cell analysis and helps users gain new insights into their research.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 31, 2020.
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scMontage: Fast and Robust Gene Expression Similarity Search for Massive Single-cell Data
Tomoya Mori, Naila Shinwari, Wataru Fujibuchi
bioRxiv 2020.08.30.271395; doi: https://doi.org/10.1101/2020.08.30.271395
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scMontage: Fast and Robust Gene Expression Similarity Search for Massive Single-cell Data
Tomoya Mori, Naila Shinwari, Wataru Fujibuchi
bioRxiv 2020.08.30.271395; doi: https://doi.org/10.1101/2020.08.30.271395

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