Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge

S Mukherjee, Y Zhang, J Fan, G Seelig… - …, 2018 - academic.oup.com
Motivation Single cell RNA-seq (scRNA-seq) data contains a wealth of information which
has to be inferred computationally from the observed sequencing reads. As the ability to …

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

V Gardeux, FPA David, A Shajkofci, PC Schwalie… - …, 2017 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of
thousands of individual cells, enabling the molecular exploration of tissues at the cellular …

Pre-processing, dimension reduction, and clustering for single-cell RNA-seq data

J Hu, Y Wang, X Zhou, M Chen - Handbook of Statistical Bioinformatics, 2022 - Springer
The advent of scRNA-seq technologies enables us to quantitatively characterize gene
expression at each single-cell level. The high resolution has thus far transformed many …

scRNA-Explorer: An end-user online tool for single cell RNA-seq data analysis featuring gene correlation and data filtering

I Baltsavia, A Oulas, T Theodosiou, MD Lavigne… - Journal of Molecular …, 2024 - Elsevier
In the majority of downstream analysis pipelines for single-cell RNA sequencing (scRNA-
seq), techniques like dimensionality reduction and feature selection are employed to …

[HTML][HTML] The impact of package selection and versioning on single-cell RNA-seq analysis

JM Rich, L Moses, PH Einarsson, K Jackson… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting
raw read data into cell-gene count matrices through sequence alignment, followed by …

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 …

Monet: An open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces

F Wagner - bioRxiv, 2020 - biorxiv.org
Single-cell RNA-Seq is a powerful technology that enables the transcriptomic profiling of the
different cell populations that make up complex tissues. However, the noisy and high …

scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis

JJ Cai - 2020 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) technology has revolutionized the way
research is done in biomedical sciences. It provides an unprecedented level of resolution …

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 …

Consequences and opportunities arising due to sparser single-cell RNA-seq datasets

GA Bouland, A Mahfouz, MJT Reinders - Genome biology, 2023 - Springer
With the number of cells measured in single-cell RNA sequencing (scRNA-seq) datasets
increasing exponentially and concurrent increased sparsity due to more zero counts being …