scVIC: Deep generative modeling of heterogeneity for scRNA-seq data

J Xiong, F Gong, L Ma, L Wan - Bioinformatics Advances, 2024 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) has become a valuable tool for
studying cellular heterogeneity. However, the analysis of scRNA-seq data is challenging …

Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data

C Cheng, J Easton, C Rosencrance, Y Li… - Nucleic Acids …, 2019 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for characterizing the cell-to-cell
variation and cellular dynamics in populations which appear homogeneous otherwise in …

Scaling up single-cell RNA-seq data analysis with CellBridge workflow

N Nouri, AH Kurlovs, G Gaglia, E de Rinaldis… - …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression
at the individual cell level, unraveling unprecedented insights into cellular heterogeneity …

Generating Synthetic Single Cell Data from Bulk RNA-seq Using a Pretrained Variational Autoencoder

HJ Cho - bioRxiv, 2024 - biorxiv.org
Single cell RNA sequencing (scRNA-seq) is a powerful approach which generates genome-
wide gene expression profiles at single cell resolution. Among its many applications, it …

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data

A Lütge, J Zyprych-Walczak… - Life science …, 2021 - life-science-alliance.org
A key challenge in single-cell RNA-sequencing (scRNA-seq) data analysis is batch effects
that can obscure the biological signal of interest. Although there are various tools and …

[PDF][PDF] Prior knowledge and sampling model informed learning with single cell rna-seq data

S Mukherjee, Y Zhang, S Kannan, G Seelig - bioRxiv, 2017 - academia.edu
Single cell RNA-seq (scRNA-seq) experiments can provide a wealth of information about
heterogeneous, multi-cellular systems. However, this information has to be inferred …

[HTML][HTML] One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data

CX Wang, L Zhang, B Wang - Genome biology, 2022 - Springer
Integrative analysis of large-scale single-cell RNA sequencing (scRNA-seq) datasets can
aggregate complementary biological information from different datasets. However, most …

scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication

Y Lin, S Ghazanfar, K Wang, JA Gagnon-Bartsch… - bioRxiv, 2018 - biorxiv.org
Concerted examination of multiple collections of single cell RNA-Seq (scRNA-Seq) data
promises further biological insights that cannot be uncovered with individual datasets …

[HTML][HTML] A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data

M Chen, A Dahl - Nature Communications, 2024 - nature.com
Single-cell RNA sequencing (scRNA-seq) has been widely used to characterize cell types
based on their average gene expression profiles. However, most studies do not consider …

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 …