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 …

CellMarker: a manually curated resource of cell markers in human and mouse

X Zhang, Y Lan, J Xu, F Quan, E Zhao… - Nucleic acids …, 2019 - academic.oup.com
One of the most fundamental questions in biology is what types of cells form different tissues
and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and …

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data

A Ianevski, AK Giri, T Aittokallio - Nature communications, 2022 - nature.com
Identification of cell populations often relies on manual annotation of cell clusters using
established marker genes. However, the selection of marker genes is a time-consuming …

[HTML][HTML] Automated methods for cell type annotation on scRNA-seq data

G Pasquini, JER Arias, P Schäfer… - Computational and …, 2021 - Elsevier
The advent of single-cell sequencing started a new era of transcriptomic and genomic
research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type …

Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets

F Pont, M Tosolini, JJ Fournié - Nucleic acids research, 2019 - academic.oup.com
The momentum of scRNA-seq datasets prompts for simple and powerful tools exploring their
meaningful signatures. Here we present Single-Cell_Signature_Explorer (https://sites …

[HTML][HTML] Automatic cell type identification methods for single-cell RNA sequencing

B Xie, Q Jiang, A Mora, X Li - Computational and Structural Biotechnology …, 2021 - Elsevier
Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for scientists of many
research disciplines due to its ability to elucidate the heterogeneous and complex cell-type …

[HTML][HTML] Identifying cell populations with scRNASeq

TS Andrews, M Hemberg - Molecular aspects of medicine, 2018 - Elsevier
Single-cell RNASeq (scRNASeq) has emerged as a powerful method for quantifying the
transcriptome of individual cells. However, the data from scRNASeq experiments is often …

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments

HA Ekiz, CJ Conley, WZ Stephens, RM O'Connell - BMC bioinformatics, 2020 - Springer
Background Single cell RNA sequencing (scRNAseq) has provided invaluable insights into
cellular heterogeneity and functional states in health and disease. During the analysis of …

scRNASeqDB: a database for RNA-Seq based gene expression profiles in human single cells

Y Cao, J Zhu, P Jia, Z Zhao - Genes, 2017 - mdpi.com
Single-cell RNA sequencing (scRNA-Seq) is rapidly becoming a powerful tool for high-
throughput transcriptomic analysis of cell states and dynamics at the single cell level. Both …

[HTML][HTML] A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines

R Nayak, Y Hasija - Genomics, 2021 - Elsevier
Single-cell transcriptomics (SCT) is a tour de force in the era of big omics data that has led to
the accumulation of massive cellular transcription data at an astounding resolution of single …