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SCHNAPPs - Single Cell sHiNy APPlication(s)
Bernd Jagla1, Valentina Libri2, Claudia Chica3
1Institut Pasteur, Université de Paris, Cytometry and Biomarkers UTechS, F-75015 Paris, France; Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France.
Journal of Immunological Methods
|November 7, 2021
Summary
SCHNAPPs is a new GUI application that simplifies single-cell RNA sequencing (scRNAseq) data analysis for bench scientists. It enables autonomous exploration and interpretation of complex scRNAseq data, fostering collaboration and reproducible research.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Single-cell RNA sequencing (scRNAseq) generates complex data requiring specialized bioinformatics expertise.
- Bench scientists need accessible tools to analyze scRNAseq data and focus on biological discovery.
- Bridging the gap between bench scientists and bioinformaticians is crucial for advancing scRNAseq research.
Purpose of the Study:
- To present SCHNAPPs, a Graphical User Interface (GUI) enabling bench scientists to autonomously analyze and interpret scRNAseq data.
- To provide a user-friendly platform that abstracts technical complexities of scRNAseq analysis.
- To facilitate reproducible science and collaboration between bench scientists and bioinformaticians.
Main Methods:
- Development of an R/Shiny-based application, SCHNAPPs, with a modular design.
- Integration of established scRNAseq analysis workflows from Seurat and Scran packages.
- Implementation of diverse visualization tools (violin plots, 2D projections, etc.) and R-markdown reporting.
Main Results:
- SCHNAPPs empowers bench scientists to perform quality control, normalization, integration, dimension reduction, clustering, and differential gene expression analysis.
- The application supports autonomous data exploration and interpretation through interactive visualizations.
- A case study on T cell characterization using scRNAseq and CITE-Seq data demonstrates SCHNAPPs' utility.
Conclusions:
- SCHNAPPs effectively lowers the barrier for bench scientists to conduct sophisticated scRNAseq data analysis.
- The tool promotes reproducible research practices and enhances collaboration in the field.
- SCHNAPPs is a valuable resource for the broader scientific community seeking to leverage scRNAseq data.
