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Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*

Booeshaghi, A. Sina and Pachter, Lior (2021) Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*. Bioinformatics, 37 (15). pp. 2223-2224. ISSN 1367-4803. PMCID PMC7989636. doi:10.1093/bioinformatics/btab085.

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Single-cell RNA-seq technologies have been successfully employed over the past decade to generate many high resolution cell atlases. These have proved invaluable in recent efforts aimed at understanding the cell type specificity of host genes involved in SARS-CoV-2 infections. While single-cell atlases are based on well-sampled highly-expressed genes, many of the genes of interest for understanding SARS-CoV-2 can be expressed at very low levels. Common assumptions underlying standard single-cell analyses don’t hold when examining low-expressed genes, with the result that standard workflows can produce misleading results.

Item Type:Article
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URLURL TypeDescription CentralArticle
Booeshaghi, A. Sina0000-0002-6442-4502
Pachter, Lior0000-0002-9164-6231
Alternate Title:log(x+1)* and log(1+x)*
Additional Information:© The Author(s) 2021. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 14 October 2020; Revision received: 23 December 2020; Editorial decision: 29 January 2021; Accepted: 01 March 2021; Published: 02 March 2021. We thank Charles Herring, Michael Hoffman, Johan Gustafsson, Harold Pimentel, Jeffrey Spence, and Valentine Svensson for helpful comments. A.S.B. and L.P. were partially funded by NIH U19MH114830. Conflict of Interest: none declared.
Funding AgencyGrant Number
Subject Keywords:single-cell, log1p, normalization, ACE2
Issue or Number:15
PubMed Central ID:PMC7989636
Record Number:CaltechAUTHORS:20200520-084505912
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Official Citation:A Sina Booeshaghi, Lior Pachter, Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x), Bioinformatics, Volume 37, Issue 15, 1 August 2021, Pages 2223–2224,
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:103346
Deposited By: Tony Diaz
Deposited On:20 May 2020 15:51
Last Modified:09 Feb 2022 20:49

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