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ezSingleCell：一个集成的一站式单细胞和空间组学分析平台，适用于实验科学家。

ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists.

机构信息

Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore.

Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.

出版信息

Nat Commun. 2024 Jul 3;15(1):5600. doi: 10.1038/s41467-024-48188-2.

DOI:10.1038/s41467-024-48188-2
PMID:38961061
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11222513/
Abstract

ezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task. In addition, ezSingleCell allows crosstalk between different modules within a unified interface. Acceptable input data can be in a variety of formats while the output consists of publication ready figures and tables. In-depth manuals and video tutorials are available to guide users on the analysis workflows and parameter adjustments to suit their study aims. ezSingleCell's streamlined interface can analyse a standard scRNA-seq dataset of 3000 cells in less than five minutes. ezSingleCell is available in two forms: an installation-free web application ( https://immunesinglecell.org/ezsc/ ) or a software package with a shinyApp interface ( https://github.com/JinmiaoChenLab/ezSingleCell2 ) for offline analysis.

摘要

ezSingleCell 是一款交互式、易于使用的应用程序，可分析各种单细胞和空间组学数据类型，而无需事先具备编程知识。它结合了性能最佳的公开可用方法，用于深入数据分析、集成和交互式数据可视化。ezSingleCell 由五个模块组成，每个模块都旨在成为一种针对特定数据类型或任务的综合工作流程。此外，ezSingleCell 允许在统一界面内的不同模块之间进行交互。可接受的输入数据可以采用多种格式，而输出则包括可发表的图形和表格。详细的手册和视频教程可指导用户进行分析工作流程和参数调整，以满足其研究目标。ezSingleCell 的简化界面可以在不到五分钟的时间内分析一个包含 3000 个细胞的标准 scRNA-seq 数据集。ezSingleCell 有两种形式：免安装的网络应用程序（https://immunesinglecell.org/ezsc/）或带有 shinyApp 接口的软件包（https://github.com/JinmiaoChenLab/ezSingleCell2），用于离线分析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/212969a37cbd/41467_2024_48188_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/f85d919f31b3/41467_2024_48188_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/a87561d7eeeb/41467_2024_48188_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/3c1a97d5b965/41467_2024_48188_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/4b92d6ead8d9/41467_2024_48188_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/ce02182306a5/41467_2024_48188_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/69d383bb0ac0/41467_2024_48188_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/3b64900a870e/41467_2024_48188_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/212969a37cbd/41467_2024_48188_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/f85d919f31b3/41467_2024_48188_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/a87561d7eeeb/41467_2024_48188_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/3c1a97d5b965/41467_2024_48188_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/4b92d6ead8d9/41467_2024_48188_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/ce02182306a5/41467_2024_48188_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/69d383bb0ac0/41467_2024_48188_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/3b64900a870e/41467_2024_48188_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/20eb/11222513/212969a37cbd/41467_2024_48188_Fig8_HTML.jpg

相似文献

[1]
ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists.

Nat Commun. 2024-7-3

[2]
Shaoxia: a web-based interactive analysis platform for single cell RNA sequencing data.

BMC Genomics. 2024-4-24

[3]
Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data.

BMC Genomics. 2019-8-27

[4]
BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization.

Nucleic Acids Res. 2020-7-2

[5]
DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics.

Int J Mol Sci. 2021-1-30

[6]
SinglePointRNA, an user-friendly application implementing single cell RNA-seq analysis software.

PLoS One. 2024

[7]
Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis.

PLoS Comput Biol. 2020-4-27

[8]
SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis.

J Comput Biol. 2021-8

[9]
Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists.

Genome Med. 2017-12-5

[10]
ascend: R package for analysis of single-cell RNA-seq data.

Gigascience. 2019-8-1

引用本文的文献

[1]
CytoAnalyst web platform facilitates comprehensive single cell RNA sequencing analysis.

Sci Rep. 2025-8-6

[2]
Comprehensive analysis of multi-omics single-cell data using the single-cell analyst.

Imeta. 2025-4-28

[3]
SCPline: An interactive framework for the single-cell proteomics data preprocessing.

Brief Bioinform. 2025-5-1

[4]
Single-cell genomics and spatial transcriptomics in islet transplantation for diabetes treatment: advancing towards personalized therapies.

Front Immunol. 2025-2-20

[5]
Mechanisms of radiation-induced tissue damage and response.

MedComm (2020). 2024-9-20

[6]
Distributed Collaboration for Data, Analysis Pipelines, and Results in Single-Cell Omics.

bioRxiv. 2024-7-30

[7]
Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis.

Mol Biol Evol. 2023-12-1

本文引用的文献

[1]
Automatic cell-type harmonization and integration across Human Cell Atlas datasets.

Cell. 2023-12-21

[2]
Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST.

Nat Commun. 2023-3-1

[3]
rGREAT: an R/bioconductor package for functional enrichment on genomic regions.

Bioinformatics. 2023-1-1

[4]
An introduction to spatial transcriptomics for biomedical research.

Genome Med. 2022-6-27

[5]
Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Science. 2022-5-13

[6]
ICARUS, an interactive web server for single cell RNA-seq analysis.

Nucleic Acids Res. 2022-7-5

[7]
Interactive single-cell data analysis using Cellar.

Nat Commun. 2022-4-14

[8]
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Nat Methods. 2022-5

[9]
Benchmarking atlas-level data integration in single-cell genomics.

Nat Methods. 2022-1

[10]
DISCO: a database of Deeply Integrated human Single-Cell Omics data.

Nucleic Acids Res. 2022-1-7

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