scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning

HS Li, L Ou-Yang, Y Zhu, H Yan… - Briefings in …, 2022 - academic.oup.com
The identification of differentially expressed genes between different cell groups is a crucial
step in analyzing single-cell RNA-sequencing (scRNA-seq) data. Even though various …

scHD4E: Novel ensemble learning-based differential expression analysis method for single-cell RNA-sequencing data

B Biswas, N Kumar, M Sugimoto, MA Hoque - Computers in Biology and …, 2024 - Elsevier
Differential expression (DE) analysis between cell types for scRNA-seq data by capturing its
complicated features is crucial. Recently, different methods have been developed for …

A comprehensive survey of statistical approaches for differential expression analysis in single-cell RNA sequencing studies

S Das, A Rai, ML Merchant, MC Cave, SN Rai - Genes, 2021 - mdpi.com
Single-cell RNA-sequencing (scRNA-seq) is a recent high-throughput sequencing
technique for studying gene expressions at the cell level. Differential Expression (DE) …

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

T Wang, B Li, CE Nelson, S Nabavi - BMC bioinformatics, 2019 - Springer
Background The analysis of single-cell RNA sequencing (scRNAseq) data plays an
important role in understanding the intrinsic and extrinsic cellular processes in biological …

[HTML][HTML] SwarnSeq: An improved statistical approach for differential expression analysis of single-cell RNA-seq data

S Das, SN Rai - Genomics, 2021 - Elsevier
Single-cell RNA sequencing (scRNA-seq) is a powerful technology that is capable of
generating gene expression data at the resolution of individual cell. The scRNA-seq data is …

Reproducibility of methods to detect differentially expressed genes from single-cell RNA sequencing

T Mou, W Deng, F Gu, Y Pawitan, TN Vu - Frontiers in genetics, 2020 - frontiersin.org
Detection of differentially expressed genes is a common task in single-cell RNA-seq (scRNA-
seq) studies. Various methods based on both bulk-cell and single-cell approaches are in …

Bias, robustness and scalability in differential expression analysis of single-cell RNA-Seq data

C Soneson, MD Robinson - bioRxiv, 2017 - biorxiv.org
Background As single-cell RNA-seq (scRNA-seq) is becoming increasingly common, the
amount of publicly available data grows rapidly, generating a useful resource for …

scCODE: an R package for data-specific differentially expressed gene detection on single-cell RNA-sequencing data

J Zou, F Deng, M Wang, Z Zhang, Z Liu… - Briefings in …, 2022 - academic.oup.com
Differential expression (DE) gene detection in single-cell ribonucleic acid (RNA)-sequencing
(scRNA-seq) data is a key step to understand the biological question investigated. Filtering …

Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies

Y Ma, S Sun, X Shang, ET Keller, M Chen… - Nature …, 2020 - nature.com
Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly
applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an …

ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data

W Zhang, Y Wei, D Zhang, EY Xu - Bioinformatics, 2020 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) has enabled the simultaneous
transcriptomic profiling of individual cells under different biological conditions. scRNA-seq …