SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

Cell Systems
Yuqi Tan, Patrick Cahan

Abstract

Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by searching for combinations of genes that have previously been implicated as being cell-type specific, an approach that is not quantitative and does not explicitly take advantage of other single-cell RNA-seq studies. Here, we describe our tool, SingleCellNet, which addresses these issues and enables the classification of query single-cell RNA-seq data in comparison to reference single-cell RNA-seq data. SingleCellNet compares favorably to other methods in sensitivity and specificity, and it is able to classify across platforms and species. We highlight SingleCellNet's utility by classifying previously undetermined cells, and by assessing the outcome of a cell fate engineering experiment.

Citations

Dec 13, 2019·Genome Biology·Jose Alquicira-HernandezJoseph E Powell
Oct 13, 2019·Science Immunology·Sven D SommerfeldJennifer H Elisseeff
Jun 26, 2020·Development·Qin BianPatrick Cahan
May 5, 2020·Briefings in Bioinformatics·Mattia ForcatoSilvio Bicciato
Sep 19, 2019·Nucleic Acids Research·Erica A K DePasqualeNathan Salomonis
May 20, 2020·Nature Methods·Zhichao MiaoSarah A Teichmann
Mar 13, 2020·APL Bioengineering·Ngan F HuangSong Li
Nov 6, 2020·Molecular Plant·Rahul ShawJian Xu
Jan 9, 2021·Cell Stem Cell·Patrick CahanChristine A Wells
Feb 24, 2021·Genome Biology·Hongyu Guo, Jun Li
Apr 7, 2021·Briefings in Bioinformatics·Zilong ZhangQuan Zou
Apr 14, 2021·Nature Communications·Shengquan ChenZhixiang Lin
May 1, 2021·Genome Medicine·Da PengPatrick Cahan
May 18, 2021·Frontiers in Oncology·Yara E Sánchez-CorralesAlice Giustacchini
Jun 25, 2021·Nature·Daniela J Di BellaPaola Arlotta
Jul 3, 2021·International Journal of Molecular Sciences·Hyun Kyu KimMan Ryul Lee
Sep 11, 2021·The American Journal of Pathology·Elisabet PujadasCarlos Cordon-Cardo
Sep 23, 2021·Nature Communications·Sheng WangRuss B Altman
Dec 29, 2020·Genomics, Proteomics & Bioinformatics·Qianhui HuangLana X Garmire
Feb 26, 2021·Genome Research·Jacob C Kimmel, David R Kelley
Oct 9, 2021·Nature Communications·Joyce B KangSoumya Raychaudhuri

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