Chevreul: An R Bioconductor Package for Exploratory Analysis of Full-Length Single Cell Sequencing

Chevreul is an open-source R Bioconductor package and interactive R Shiny app for processing and visualization of single cell RNA sequencing (scRNA-seq) data. It differs from other scRNA- seq analysis packages in its ease of use, its capacity to analyze full-length RNA sequencing data for exon coverage and transcript isoform inference, and its support for batch correction. Chevreul enables exploratory analysis of scRNA-seq data using Bioconductor SingleCellExperiment or Seurat objects. Simple processing functions with sensible default settings enable batch integration, quality control filtering, read count normalization and transformation, dimensionality reduction, clustering at a range of resolutions, and cluster marker gene identification. Processed data can be visualized in an interactive R Shiny app with dynamically linked plots. Expression of gene or transcript features can be displayed on PCA, tSNE, and UMAP embeddings, heatmaps, or violin plots while differential expression can be evaluated with several statistical tests without extensive programming. Existing analysis tools do not provide specialized tools for isoform-level analysis or alternative splicing detection. By enabling isoform-level expression analysis for differential expression, dimensionality reduction and batch integration, Chevreul empowers researchers without prior programming experience to analyze full-length scRNA-seq data. Data availabilityA test dataset formatted as a SingleCellExperiment object can be found at https://github.com/cobriniklab/chevreuldata. Availability & ImplementationChevreul is implemented in R and the R package and integrated Shiny application are freely available at https://github.com/cobriniklab/chevreul.