ezSinglecell : An integrated one-stop single-cell and spatial analysis toolbox for bench scientists
ezSingleCell is an integrated one-stop single-cell and spatial analysis toolbox developed by Chen Jinmiao's lab with an intention to empower bench scientists to perform downstream Bioinformatics analysis. In the current version, we incorporate 5 modules : Single cell RNA-seq, Single cell Data Integration, Single cell Multiomics, Single Cell ATAC-seq and Spatial Transcriptomics.
In this web server, we combine in-house novel algorithms such as CELLiD (for cell type identification), along with existing top performing methods for both basic and advanced downstream analyses such as batch effect removal, trajectory, cell-cell communication, differential abundance, and spatial deconvolution.
Currently ezSingleCell supports inputs in different formats such as text, csv or 10X cell ranger output. ezSingleCell is also available as a software package with a ShinyApp interface ,that can be run on a computer with basic memory requirements
The toolkit uses example data from DISCO that contains data from 13998 samples, covering 461 tissues/cell lines/organoids, 158 diseases, and 20 platforms.
Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR)
Github: https://github.com/JinmiaoChenLab/
Created by Jinmiao Chen Lab and collaborated with Vishuo Biomedical Pte. Ltd.
Workflow for scRNA-Seq module
Load your example data
Load your example data
Load your example data
Load your example data
Quality control
Determine cluster resolution:
Subcluster Analysis
Please modify your celltypes below:
UMAP with renamed celltypes
Not supported yet
Interacting partners
Workflow for Data Integration module
Load your example data
Load your example data
Load your input data
Quality control
Determine cluster resolution:
Subcluster Analysis
Interacting partners
Workflow for Spatial Transcriptomics module
Load your example data
Load your example data
Load your example data
Quality control
Spatial counts
H&E Image
Spatial counts
H&E Image
Spatial counts
H&E Image
Workflow for scMultiomics module
Load example data
Load example data
Quality control
RNA QC
ADT QC
RNA QC
ATAC QC
RNA Data
ADT/ATAC Data
RNA Data
ADT/ATAC Data
Workflow for scATAC-Seq module
Load your example data
ATAC counts