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Asc-Seurat: analytical single-cell Seurat-based web application.

W J Pereira1, F M Almeida2, D Conde3

  • 1School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA. wendelljpereira@gmail.com.

BMC Bioinformatics
|November 19, 2021
PubMed
Summary
This summary is machine-generated.

Asc-Seurat offers a user-friendly web application for single-cell RNA sequencing (scRNA-seq) analysis. This tool simplifies complex data interpretation, reducing biologist

Keywords:
Gene expressionSingle-cell RNA sequencingWeb applicationscRNA-seq

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Single-cell RNA sequencing (scRNA-seq) is a powerful technology for transcriptome analysis and cell type discovery.
  • scRNA-seq data analysis is complex, requiring specialized tools for data refinement and biological insight extraction.
  • A need exists for an integrated, user-friendly platform to streamline the entire scRNA-seq analysis workflow.

Purpose of the Study:

  • To develop Asc-Seurat, a comprehensive and accessible web application for scRNA-seq data analysis.
  • To provide a user-friendly interface for critical scRNA-seq analysis steps, including quality control, clustering, and differential gene expression.
  • To integrate advanced modules for trajectory inference (pseudotime analysis) and functional gene annotation.

Main Methods:

  • Asc-Seurat is a web application built upon the Seurat package.
  • It incorporates functions for data quality control, clustering, and differential gene expression analysis.
  • Includes modules for pseudotime inference using various models and gene ontology enrichment analysis.

Main Results:

  • Asc-Seurat provides a feature-rich workbench with an intuitive graphical interface.
  • The application successfully analyzes peripheral blood mononuclear cell data, demonstrating its capabilities.
  • It streamlines the analysis of scRNA-seq data, making it more accessible to biologists.

Conclusions:

  • Asc-Seurat offers a comprehensive solution for scRNA-seq data analysis with an accessible graphical interface.
  • The platform significantly reduces the time and effort required for analyzing and interpreting scRNA-seq datasets.
  • Asc-Seurat empowers biologists to conduct complex analyses independently.