Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data

L Yu, Y Cao, JYH Yang, P Yang - Genome biology, 2022 - Springer
Background A key task in single-cell RNA-seq (scRNA-seq) data analysis is to accurately
detect the number of cell types in the sample, which can be critical for downstream analyses …

Identification of cell types from single cell data using stable clustering

A Peyvandipour, A Shafi, N Saberian, S Draghici - Scientific reports, 2020 - nature.com
Single-cell RNA-seq (scRNASeq) has become a powerful technique for measuring the
transcriptome of individual cells. Unlike the bulk measurements that average the gene …

Consensus clustering of single-cell RNA-seq data by enhancing network affinity

Y Cui, S Zhang, Y Liang, X Wang… - Briefings in …, 2021 - academic.oup.com
Elucidation of cell subpopulations at high resolution is a key and challenging goal of single-
cell ribonucleic acid (RNA) sequencing (scRNA-seq) data analysis. Although unsupervised …

Accurate feature selection improves single-cell RNA-seq cell clustering

K Su, T Yu, H Wu - Briefings in bioinformatics, 2021 - academic.oup.com
Cell clustering is one of the most important and commonly performed tasks in single-cell
RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select …

SAFE-clustering: single-cell aggregated (from ensemble) clustering for single-cell RNA-seq data

Y Yang, R Huh, HW Culpepper, Y Lin, MI Love… - …, 2019 - academic.oup.com
Motivation Accurately clustering cell types from a mass of heterogeneous cells is a crucial
first step for the analysis of single-cell RNA-seq (scRNA-Seq) data. Although several …

Impact of similarity metrics on single-cell RNA-seq data clustering

T Kim, IR Chen, Y Lin, AYY Wang… - Briefings in …, 2019 - academic.oup.com
Advances in high-throughput sequencing on single-cell gene expressions [single-cell RNA
sequencing (scRNA-seq)] have enabled transcriptome profiling on individual cells from …

Machine learning and statistical methods for clustering single-cell RNA-sequencing data

R Petegrosso, Z Li, R Kuang - Briefings in bioinformatics, 2020 - academic.oup.com
Single-cell RNAsequencing (scRNA-seq) technologies have enabled the large-scale whole-
transcriptome profiling of each individual single cell in a cell population. A core analysis of …

Benchmark and parameter sensitivity analysis of single-cell RNA sequencing clustering methods

M Krzak, Y Raykov, A Boukouvalas, L Cutillo… - Frontiers in …, 2019 - frontiersin.org
Single-cell RNA-seq (scRNAseq) is a powerful tool to study heterogeneity of cells. Recently,
several clustering based methods have been proposed to identify distinct cell populations …

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis

TA Geddes, T Kim, L Nan, JG Burchfield, JYH Yang… - BMC …, 2019 - Springer
Background Single-cell RNA-sequencing (scRNA-seq) is a transformative technology,
allowing global transcriptomes of individual cells to be profiled with high accuracy. An …

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data

M Barron, J Li - Scientific reports, 2016 - nature.com
Abstract Single-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for
discovering and describing cell types in heterogeneous tissues, yet its measurement of …