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SciBet as a portable and fast single cell type identifier

Author

Listed:
  • Chenwei Li

    (Peking University
    Analytical Biosciences Limited)

  • Baolin Liu

    (Peking University
    Peking University)

  • Boxi Kang

    (Peking University
    Analytical Biosciences Limited
    Peking University)

  • Zedao Liu

    (Peking University
    Analytical Biosciences Limited)

  • Yedan Liu

    (Peking University
    Peking University)

  • Changya Chen

    (Children’s Hospital of Philadelphia)

  • Xianwen Ren

    (Peking University
    Peking University)

  • Zemin Zhang

    (Peking University
    Analytical Biosciences Limited
    Peking University)

Abstract

Fast, robust and technology-independent computational methods are needed for supervised cell type annotation of single-cell RNA sequencing data. We present SciBet, a supervised cell type identifier that accurately predicts cell identity for newly sequenced cells with order-of-magnitude speed advantage. We enable web client deployment of SciBet for rapid local computation without uploading local data to the server. Facing the exponential growth in the size of single cell RNA datasets, this user-friendly and cross-platform tool can be widely useful for single cell type identification.

Suggested Citation

  • Chenwei Li & Baolin Liu & Boxi Kang & Zedao Liu & Yedan Liu & Changya Chen & Xianwen Ren & Zemin Zhang, 2020. "SciBet as a portable and fast single cell type identifier," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15523-2
    DOI: 10.1038/s41467-020-15523-2
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    Cited by:

    1. Laura K. Hamilton & Gaël Moquin-Beaudry & Chenicka L. Mangahas & Federico Pratesi & Myriam Aubin & Anne Aumont & Sandra E. Joppé & Alexandre Légiot & Annick Vachon & Mélanie Plourde & Catherine Mounie, 2022. "Stearoyl-CoA Desaturase inhibition reverses immune, synaptic and cognitive impairments in an Alzheimer’s disease mouse model," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Augusto Faria Andrade & Alva Annett & Elham Karimi & Danai Georgia Topouza & Morteza Rezanejad & Yitong Liu & Michael McNicholas & Eduardo G. Gonzalez Santiago & Dhana Llivichuzhca-Loja & Arne Gehlhaa, 2024. "Immune landscape of oncohistone-mutant gliomas reveals diverse myeloid populations and tumor-promoting function," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Jiawei Chen & Hao Xu & Wanyu Tao & Zhaoxiong Chen & Yuxuan Zhao & Jing-Dong J. Han, 2023. "Transformer for one stop interpretable cell type annotation," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Rongbo Shen & Lin Liu & Zihan Wu & Ying Zhang & Zhiyuan Yuan & Junfu Guo & Fan Yang & Chao Zhang & Bichao Chen & Wanwan Feng & Chao Liu & Jing Guo & Guozhen Fan & Yong Zhang & Yuxiang Li & Xun Xu & Ji, 2022. "Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Xin Li & Bairu Li & Shaobin Gu & Xinyue Pang & Patrick Mason & Jiangfeng Yuan & Jingyu Jia & Jiaju Sun & Chunyan Zhao & Robert Henry, 2024. "Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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