constclust: consistent clusters for scRNA-seq

I Virshup, J Choi, KA Lê Cao, CA Wells - bioRxiv, 2020 - biorxiv.org
Unsupervised clustering to identify distinct cell types is a crucial step in the analysis of
scRNA-seq data. Current clustering methods are dependent on a number of parameters …

UICPC: centrality-based clustering for scRNA-seq data analysis without user input

HA Chowdhury, DK Bhattacharyya, JK Kalita - Computers in Biology and …, 2021 - Elsevier
Abstract scRNA-seq data analysis enables new possibilities for identification of novel cells,
specific characterization of known cells and study of cell heterogeneity. The performance of …

Robust clustering and interpretation of scRNA-seq data using reference component analysis

F Schmidt, B Ranjan, QXX Lin, V Krishnan, I Joanito… - bioRxiv, 2021 - biorxiv.org
Motivation The transcriptomic diversity of the hundreds of cell types in the human body can
be analysed in unprecedented detail using single cell (SC) technologies. Though clustering …

scCNC: a method based on capsule network for clustering scRNA-seq data

HY Wang, JP Zhao, CH Zheng, YS Su - Bioinformatics, 2022 - academic.oup.com
Motivation A large number of studies have shown that clustering is a crucial step in scRNA-
seq analysis. Most existing methods are based on unsupervised learning without the prior …

scMUSCL: Multi-Source Transfer Learning for Clustering scRNA-seq Data

A Khoeini, F Sar, YY Lin, C Collins, M Ester - bioRxiv, 2024 - biorxiv.org
scRNA-seq analysis relies heavily on single-cell clustering to perform many downstream
functions. Several machine learning methods have been proposed to improve the clustering …

Clustering deviation index (CDI): a robust and accurate unsupervised measure for evaluating scRNA-seq data clustering

J Fang, C Chan, K Owzar, L Wang, D Qin, QJ Li, J Xie - bioRxiv, 2022 - biorxiv.org
Single-cell RNA-sequencing (scRNA-seq) technology allows us to explore cellular
heterogeneity in the transcriptome. Because most scRNA-seq data analyses begin with cell …

scNAME: neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data

H Wan, L Chen, M Deng - Bioinformatics, 2022 - academic.oup.com
Motivation The rapid development of single-cell RNA sequencing (scRNA-seq) makes it
possible to study the heterogeneity of individual cell characteristics. Cell clustering is a vital …

scSemiAAE: a semi-supervised clustering model for single-cell RNA-seq data

Z Wang, H Wang, J Zhao, C Zheng - BMC bioinformatics, 2023 - Springer
Background Single-cell RNA sequencing (scRNA-seq) strives to capture cellular diversity
with higher resolution than bulk RNA sequencing. Clustering analysis is critical to …

Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis

J Kubovčiak, M Kolář, J Novotný - Bioinformatics Advances, 2023 - academic.oup.com
Motivation While the workflow for primary analysis of single-cell RNA-seq (scRNA-seq) data
is well established, the secondary analysis of the feature-barcode matrix is usually done by …

Clustering scRNA-seq data via qualitative and quantitative analysis

D Li, Q Mei, G Li - bioRxiv, 2023 - biorxiv.org
Single-cell RNA sequencing (scRNA-seq) technologies have been driving the development
of algorithms of clustering heterogeneous cells. We introduce a novel clustering algorithm …