SciBet: a portable and fast single cell type identifier

Fast, robust and technology-independent computational methods are needed for supervised cell type annotation of single-cell RNA sequencing data. We present SciBet, a Bayesian classifier that accurately predicts cell identity for newly sequenced cells or cell clusters. We enable web client deployment of SciBet for rapid local computation without uploading local data to the server. This user-friendly and cross-platform tool can be widely useful for single cell type identification.

[1]  Lai Guan Ng,et al.  Dimensionality reduction for visualizing single-cell data using UMAP , 2018, Nature Biotechnology.

[2]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[3]  Monika S. Kowalczyk,et al.  A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade , 2018, Cell.

[4]  Christoph Hafemeister,et al.  Comprehensive integration of single cell data , 2018, bioRxiv.

[5]  James T. Webber,et al.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018, Nature.

[6]  Martin Hemberg,et al.  M3Drop: dropout-based feature selection for scRNASeq , 2018, Bioinform..

[7]  Samuel L. Wolock,et al.  A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. , 2016, Cell systems.

[8]  M. Hemberg,et al.  scmap: projection of single-cell RNA-seq data across data sets , 2018, Nature Methods.

[9]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[10]  Mauro J. Muraro,et al.  A Single-Cell Transcriptome Atlas of the Human Pancreas , 2016, Cell systems.

[11]  Gary D Bader,et al.  Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations , 2018, Nature Communications.

[12]  Principal Investigators,et al.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018 .

[13]  Joonsoo Kang,et al.  Immunological Genome Project and systems immunology. , 2013, Trends in immunology.

[14]  Nancy R. Zhang,et al.  SAVER: Gene expression recovery for single-cell RNA sequencing , 2018, Nature Methods.

[15]  Hava T. Siegelmann,et al.  Support Vector Clustering , 2002, J. Mach. Learn. Res..

[16]  Fabian J Theis,et al.  The Human Cell Atlas , 2017, bioRxiv.

[17]  Lin Wei,et al.  Cell BLAST: Searching large-scale scRNA-seq databases via unbiased cell embedding , 2019, bioRxiv.

[18]  J. Schug,et al.  Single-Cell Transcriptomics of the Human Endocrine Pancreas , 2016, Diabetes.