Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST

Single-cell RNA-seq (scRNA-seq) is being widely used to resolve cellular heterogeneity. Here, the authors present a cell-querying method built on a neural network-based generative model and a customized cell-to-cell similarity metric.

Bibliographic Details
Main Authors:	Zhi-Jie Cao, Lin Wei, Shen Lu, De-Chang Yang, Ge Gao
Format:	Article
Language:	English
Published:	Nature Publishing Group 2020-07-01
Series:	Nature Communications
Online Access:	https://doi.org/10.1038/s41467-020-17281-7

Similar Items

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.
by: Luke Zappia, et al.
Published: (2018-06-01)

Using DenseFly algorithm for cell searching on massive scRNA-seq datasets
by: Yixin Chen, et al.
Published: (2020-12-01)

Revealing cell fate decisions during reprogramming by scRNA-seq
by: Liang Yu
Published: (2020-01-01)

Automated methods for cell type annotation on scRNA-seq data
by: Giovanni Pasquini, et al.
Published: (2021-01-01)

A reference-free approach for cell type classification with scRNA-seq
by: Qi Sun, et al.
Published: (2021-08-01)

Contrastive self-supervised clustering of scRNA-seq data
by: Ciortan, M., et al.
Published: (2021)

Contrastive self-supervised clustering of scRNA-seq data
by: Madalina Ciortan, et al.
Published: (2021-05-01)

Discovering single-cell eQTLs from scRNA-seq data only
by: Li, H., et al.
Published: (2022)

Single-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations
by: Wang M, et al.
Published: (2021-10-01)

Identify differential genes and cell subclusters from time-series scRNA-seq data using scTITANS
by: Li Shao, et al.
Published: (2021-01-01)

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
by: Nelson Johansen, et al.
Published: (2019-08-01)

AAE-SC: A scRNA-Seq Clustering Framework Based on Adversarial Autoencoder
by: Yulun Wu, et al.
Published: (2020-01-01)

Iterative point set registration for aligning scRNA-seq data.
by: Amir Alavi, et al.
Published: (2020-10-01)

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
by: N. M. Prashant, et al.
Published: (2021-09-01)

Effect of doxorubicin exposure in breast cancer on single-cell level by scRNA-seq analysis
by: Lladós Armengol, Núria
Published: (2021)

NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data
by: Jiankang Xiong, et al.
Published: (2020-10-01)

Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen
by: Qingkai Song, et al.
Published: (2020-06-01)

Inferring TF activation order in time series scRNA-Seq studies.
by: Chieh Lin, et al.
Published: (2020-02-01)

Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data
by: Carlos Torroja, et al.
Published: (2019-10-01)

Obstacles to detecting isoforms using full-length scRNA-seq data
by: Jennifer Westoby, et al.
Published: (2020-03-01)

Boosting scRNA-seq data clustering by cluster-aware feature weighting
by: Rui-Yi Li, et al.
Published: (2021-06-01)

COTAN: ScRNA-seq data analysis based on gene co-expression
by: Cremisi, F., et al.
Published: (2021)

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.
by: Camden Jansen, et al.
Published: (2019-11-01)

Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process.
by: Jifan Shi, et al.
Published: (2019-11-01)

Time-Resolved scRNA-Seq Tracks the Adaptation of a Sensitive MCL Cell Line to Ibrutinib Treatment
by: Viktoria Fuhr, et al.
Published: (2021-02-01)

Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance
by: Eun-Ah Christine Song, et al.
Published: (2018-09-01)

Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage
by: Kathrin Witmer, et al.
Published: (2021-03-01)

Corrigendum: Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data
by: Carlos Torroja, et al.
Published: (2020-02-01)

An efficient scRNA-seq dropout imputation method using graph attention network
by: Cai, L., et al.
Published: (2021)

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets
by: Inbal Shainer, et al.
Published: (2021-09-01)

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.
by: Charlotte Soneson, et al.
Published: (2021-01-01)

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets
by: Hongyu Liu, et al.
Published: (2021-01-01)

Integration of scRNA-Seq and Bulk RNA-Seq to Analyse the Heterogeneity of Ovarian Cancer Immune Cells and Establish a Molecular Risk Model
by: Leilei Liang, et al.
Published: (2021-09-01)

Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in mice
by: Zhengpin Wang, et al.
Published: (2019-11-01)

ScRNA-seq revealed the kinetic of nasopharyngeal immune responses in asymptomatic COVID-19 carriers
by: Furong Qi, et al.
Published: (2021-07-01)

Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers.
by: Yu Hu, et al.
Published: (2020-06-01)

A rank-based marker selection method for high throughput scRNA-seq data
by: Alexander H. S. Vargo, et al.
Published: (2020-10-01)

SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model
by: Yan Zheng, et al.
Published: (2021-01-01)

SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model
by: Hu, J., et al.
Published: (2021)

Double-jeopardy: scRNA-seq doublet/multiplet detection using multi-omic profiling
by: Bo Sun, et al.
Published: (2021-05-01)