Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

被引：114
作者：
Deng, Yue [1 ]
Bao, Feng [2 ]
Dai, Qionghai [2 ]
Wu, Lani F. [1 ]
Altschuler, Steven J. [1 ]
机构：
[1] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA 94143 USA
[2] Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Dept Automat, Beijing, Peoples R China
来源：
NATURE METHODS | 2019年 / 16卷 / 04期
关键词：
NETWORK;
D O I：
10.1038/s41592-019-0353-7
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Recent advances in large-scale single-cell RNA-seq enable fine-grained characterization of phenotypically distinct cellular states in heterogeneous tissues. We present scScope, a scalable deep-learning-based approach that can accurately and rapidly identify cell-type composition from millions of noisy single-cell gene-expression profiles.
引用
收藏
页码：311 / +
页数：7
相关论文
共 27 条
  • [1] Integrating single-cell transcriptomic data across different conditions, technologies, and species
    Butler, Andrew
    Hoffman, Paul
    Smibert, Peter
    Papalexi, Efthymia
    Satija, Rahul
    [J]. NATURE BIOTECHNOLOGY, 2018, 36 (05) : 411 - +
  • [2] Efficient Generation of Transcriptomic Profiles by Random Composite Measurements
    Cleary, Brian
    Le Cong
    Cheung, Anthea
    Lander, Eric S.
    Regev, Aviv
    [J]. CELL, 2017, 171 (06) : 1424 - +
  • [3] Single-cell RNA-seq denoising using a deep count autoencoder
    Eraslan, Goekcen
    Simon, Lukas M.
    Mircea, Maria
    Mueller, Nikola S.
    Theis, Fabian J.
    [J]. NATURE COMMUNICATIONS, 2019, 10 (1)
  • [4] Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
    Franke, Lude
    van Bakel, Harm
    Fokkens, Like
    de Jong, Edwin D.
    Egmont-Petersen, Michael
    Wijmenga, Cisca
    [J]. AMERICAN JOURNAL OF HUMAN GENETICS, 2006, 78 (06) : 1011 - 1025
  • [5] Single-cell genome sequencing: current state of the science
    Gawad, Charles
    Koh, Winston
    Quake, Stephen R.
    [J]. NATURE REVIEWS GENETICS, 2016, 17 (03) : 175 - 188
  • [6] A single-cell survey of the small intestinal epithelium
    Haber, Adam L.
    Biton, Moshe
    Rogel, Noga
    Herbst, Rebecca H.
    Shekhar, Karthik
    Smillie, Christopher
    Burgin, Grace
    Delorey, Toni M.
    Howitt, Michael R.
    Katz, Yarden
    Tirosh, Itay
    Beyaz, Semir
    Dionne, Danielle
    Zhang, Mei
    Raychowdhury, Raktima
    Garrett, Wendy S.
    Rozenblatt-Rosen, Orit
    Shi, Hai Ning
    Yilmaz, Omer
    Xavier, Ramnik J.
    Regev, Aviv
    [J]. NATURE, 2017, 551 (7680) : 333 - +
  • [7] Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
    Haghverdi, Laleh
    Lun, Aaron T. L.
    Morgan, Michael D.
    Marioni, John C.
    [J]. NATURE BIOTECHNOLOGY, 2018, 36 (05) : 421 - +
  • [8] Mapping the Mouse Cell Atlas by Microwell-Seq
    Han, Xiaoping
    Wang, Renying
    Zhou, Yincong
    Fei, Lijiang
    Sun, Huiyu
    Lai, Shujing
    Saadatpour, Assieh
    Zhou, Zimin
    Chen, Haide
    Ye, Fang
    Huang, Daosheng
    Xu, Yang
    Huang, Wentao
    Jiang, Mengmeng
    Jiang, Xinyi
    Mao, Jie
    Chen, Yao
    Lu, Chenyu
    Xie, Jin
    Fang, Qun
    Wang, Yibin
    Yue, Rui
    Li, Tiefeng
    Huang, He
    Orkin, Stuart H.
    Yuan, Guo-Cheng
    Chen, Ming
    Guo, Guoji
    [J]. CELL, 2018, 172 (05) : 1091 - +
  • [9] COMPARING PARTITIONS
    HUBERT, L
    ARABIE, P
    [J]. JOURNAL OF CLASSIFICATION, 1985, 2 (2-3) : 193 - 218
  • [10] Jeon CJ, 1998, J NEUROSCI, V18, P8936
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