Annotating single cell datasets

Tutorial: guidelines for annotating single-cell transcriptomic maps ...

Single-cell transcriptomics data are often presented as a two-dimensional 'map' organizing cells on the basis of the similarity of their gene ...

How can I annotate the cell types from scRNA-seq data?

Seurat's find.markers() function · scmap: projection of single-cell RNA-seq data across data sets · SingleR: reference-based single-cell RNA-seq annotation ...

singleCellBase: a high-quality manually curated database of cell ...

Overall, the singleCellBase database serves as a valuable resource for exploring markers associated with diverse cell types across multiple ...

Chapter 7 Cell type annotation | Basics of Single-Cell Analysis with ...

A single-cell reference preserves the “shape” of the subpopulation in high-dimensional expression space, potentially yielding more accurate predictions when the ...

Web Resources for Cell Type Annotation - 10x Genomics

To annotate your own datasets, you can select the relevant tissue type and input the top differentially expressed genes in your clusters to find which type of ...

11. Annotation - Single-cell best practices

The process of labeling groups of cells in your data based on known (or sometimes unknown) cellular phenotypes is called “cell annotation”.

Annotation of cell types (ACT): a convenient web server for cell type ...

Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At ...

a comprehensive resource for single-cell transcriptomic annotation

CellSTAR allows for the association of gene expression profiles between reference datasets and unknown cells in query datasets through ...

New machine learning-based single-cell search engine makes cell ...

It's basically a search engine. You give it a cell, and it shows you similar cells. And when you give it a single-cell dataset, it generates ...

scAnnotate: an automated cell-type annotation tool for single-cell ...

Hence, the first step of scRNA-seq data analysis is often to distinguish cell types so they can be investigated separately. Researchers have recently developed ...

Manual annotation of cell types in single cell RNA-seq - Biostars

After this, they define a set of genes and the corresponding cell types and use that to annotate their dataset. I wanted to apply the same ...

Assessing GPT-4 for cell type annotation in single-cell RNA-seq ...

Cell type annotation is a fundamental step in single-cell RNA sequencing (scRNA-seq) analysis. This process is often laborious and time- ...

Most accurate way to annotate cell identities in single cell data set ...

I feel like simply looking at marker genes is the most naive approach to annotate cells, in particular when just looking at entire clusters.

Using SingleR to annotate single-cell RNA-seq data - Bioconductor

SingleR is an automatic annotation method for single-cell RNA sequencing (scRNAseq) data (Aran et al. 2019). Given a reference dataset of ...

SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data

The SCSA algorithm is a three-step procedure that includes marker genes identification, annotation model construction, and GO enrichment analysis (Figure 1).

Annotating cell types in human single-cell RNA-seq data with CellO

CellO is a machine-learning-based tool for annotating cells using the Cell Ontology, a rich hierarchy of known cell types.

guidelines for manual cell type annotation of single-cell multi-omics ...

Although annotation workflows for datasets built with a single modality are well established, limitations exist in annotating cell types in ...

Automatic cell-annotation for single-cell RNA-Seq data - YouTube

Continuing the discussion from previous video about cell type annotation, in this video I walk through various strategies to perform cell ...

scMAGIC: accurately annotating single cells using two rounds of ...

Here, we introduce scMAGIC (Single Cell annotation using MArker Genes Identification and two rounds of reference-based Classification [RBC]), a ...

Automated methods for cell type annotation on scRNA-seq data

The advent of single-cell sequencing started a new era of transcriptomic and genomic research, advancing our knowledge of the cellular heterogeneity and ...