Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

Single-cell RNA-seq technologies and related computational data analysis

G Chen, B Ning, T Shi - Frontiers in genetics, 2019 - frontiersin.org
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …

CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data

C Hu, T Li, Y Xu, X Zhang, F Li, J Bai… - Nucleic acids …, 2023 - academic.oup.com
Abstract CellMarker 2.0 (http://bio-bigdata. hrbmu. edu. cn/CellMarker or http://117.50.
127.228/CellMarker/) is an updated database that provides a manually curated collection of …

[HTML][HTML] An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission

J Ding, JJ Garber, A Uchida, A Lefkovith… - Nature …, 2024 - nature.com
Coordinated cell interactions within the esophagus maintain homeostasis, and disruption
can lead to eosinophilic esophagitis (EoE), a chronic inflammatory disease with poorly …

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

C Hafemeister, R Satija - Genome biology, 2019 - Springer
Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to
technical factors, including the number of molecules detected in each cell, which can …

Current best practices in single‐cell RNA‐seq analysis: a tutorial

MD Luecken, FJ Theis - Molecular systems biology, 2019 - embopress.org
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …