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

• Published in: BMC bioinformatics Vol. 22; no. 1; p. 556
• Main Authors: Pereira, W J, Almeida, F M, Conde, D, Balmant, K M, Triozzi, P M, Schmidt, H W, Dervinis, C, Pappas, Jr, G J, Kirst, M
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18-11-2021; BioMed Central; Springer Science + Business Media; BMC
• Subjects: Analysis; Annotations; Applications programs; Biodiversity; Cluster Analysis; Clustering; Data analysis; Datasets; Gene expression; Gene Expression Profiling; Gene sequencing; Genomics; Internet software; Iterative methods; Leukocytes, Mononuclear; Management; Methods; Modules; Peripheral blood; Quality control; RNA sequencing; scRNA-seq; Sequence Analysis, RNA; Single-Cell Analysis; Single-cell RNA sequencing; Software; Trajectory analysis; Transcriptomes; User interface; Web application; Web applications; Workbenches; United States; scRNA-seq; Gene expression; Single-cell RNA sequencing; Web application
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04472-2

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat's capabilities by analyzing a peripheral blood mononuclear cell dataset.
Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.