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 …

ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders

AA Heydari, OA Davalos, L Zhao, KK Hoyer… - …, 2022 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNAseq) technologies allow for measurements
of gene expression at a single-cell resolution. This provides researchers with a tremendous …

Addressing the looming identity crisis in single cell RNA-seq

M Crow, A Paul, S Ballouz, ZJ Huang, J Gillis - bioRxiv, 2017 - biorxiv.org
Single cell RNA-sequencing technology (scRNA-seq) provides a new avenue to discover
and characterize cell types, but the experiment-specific technical biases and analytic …

[HTML][HTML] Integrating single-cell RNA-seq datasets with substantial batch effects

K Hrovatin, AA Moinfar, L Zappia, AT Lapuerta… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Integration of single-cell RNA-sequencing (scRNA-seq) datasets has become a standard
part of the analysis, with conditional variational autoencoders (cVAE) being among the most …

One Cell At a Time: A Unified Framework to Integrate and Analyze Single-cell RNA-seq Data

CX Wang, L Zhang, B Wang - bioRxiv, 2021 - biorxiv.org
The surge of single-cell RNA sequencing technologies gives rise to the abundance of large
single-cell RNA-seq datasets at the scale of hundreds of thousands of single cells …

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 …

Reliable and accurate gene expression quantification with subpopulation structure-aware constraints for single-cell RNA sequencing

CC Tu, JH Hung - bioRxiv, 2022 - biorxiv.org
Background Single-cell RNA sequencing (scRNA-seq) analysis analyzes the type and state
of individual cells by estimating the gene expression of each cell and enables researchers to …

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 …

Massive single-cell RNA-seq analysis and imputation via deep learning

Y Deng, F Bao, Q Dai, LF Wu, SJ Altschuler - BioRxiv, 2018 - biorxiv.org
Recent advances in large-scale single cell RNA-seq enable fine-grained characterization of
phenotypically distinct cellular states within heterogeneous tissues. We present scScope, a …

COMSE: Analysis of Single-Cell RNA-seq Data Using Community Detection Based Feature Selection

Q Luo, Y Chen, X Lan - bioRxiv, 2023 - biorxiv.org
Single-cell RNA sequencing enables studying cells individually, yet high gene dimensions
and low cell numbers challenge the analysis. And only a subset of the genes detected are …