SCHNAPPs - Single Cell sHiNy APPlication(s)

Bernd Jagla (1, 2) , Valentina Libri (1) , Claudia Chica (2) , Vincent Rouilly (3) , Sebastien Mella (1, 2) , Michel Puceat (4) , Milena Hasan (1)

1 UTechS CB - Cytometrie et Biomarqueurs – Cytometry and Biomarkers
2 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
3 Datactix
4 MMG - Marseille medical genetics - Centre de génétique médicale de Marseille

Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed to guide the investigation. Thus, there is an increasing need to develop applications geared towards bench-scientists to help them abstract the technical challenges of the analysis so that they can focus on the science at play. It is also expected that such applications should support closer collaboration between bioinformaticians and bench-scientists by providing reproducible science tools. We present SCHNAPPs, a Graphical User Interface (GUI), designed to enable bench-scientists to autonomously explore and interpret scRNAseq data and associated annotations. The R/Shiny-based application allows following different steps of scRNAseq analysis workflows from Seurat or Scran packages: performing quality control on cells and genes, normalizing the expression matrix, integrating different samples, dimension reduction, clustering, and differential gene expression analysis. Visualization tools for exploring each step of the process include violin plots, 2D projections, Box-plots, alluvial plots, and histograms. An R-markdown report can be generated that tracks modifications and selected visualizations. The modular design of the tool allows it to easily integrate new visualizations and analyses by bioinformaticians. We illustrate the main features of the tool by applying it to the characterization of T cells in a scRNAseq and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) experiment of two healthy individuals.

Mots clés: CITE-Seq; Shiny application; multi-omics data analysis; scRNA-seq

Domaines: Bio-informatique [q-bio.QM]

Bernd Jagla, Valentina Libri, Claudia Chica, Vincent Rouilly, Sebastien Mella, et al.. SCHNAPPs - Single Cell sHiNy APPlication(s). Journal of Immunological Methods, 2021, 499, pp.113176. ⟨10.1016/j.jim.2021.113176⟩. ⟨pasteur-03478264⟩