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Chevreul: An R Bioconductor Package for Exploratory Analysis of Full-Length Single Cell Sequencing
Kevin Stachelek1,2, Bhavana Bhat1, David Cobrinik1,3,4,5
1The Vision Center, Department of Surgery, and Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.
Biorxiv : the Preprint Server for Biology
|June 12, 2025
Summary
Chevreul is a new R package for single-cell RNA sequencing (scRNA-seq) analysis. It offers user-friendly tools for full-length transcript analysis, batch correction, and visualization, empowering researchers without extensive programming experience.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Single-cell RNA sequencing (scRNA-seq) generates high-dimensional data requiring specialized analysis tools.
- Existing scRNA-seq packages often lack comprehensive support for full-length transcript analysis and isoform inference.
- User-friendly interfaces are crucial for broader accessibility in scRNA-seq data analysis.
Purpose of the Study:
- To introduce Chevreul, an open-source R package and Shiny app for scRNA-seq data processing and visualization.
- To provide advanced capabilities for full-length RNA sequencing data analysis, including exon coverage and transcript isoform inference.
- To facilitate batch correction and enable exploratory data analysis for researchers with varying programming expertise.
Main Methods:
- Development of an R package and an interactive R Shiny application.
- Implementation of functions for batch integration, quality control, normalization, dimensionality reduction, and clustering.
- Integration of visualization tools for displaying gene/transcript expression on various embeddings (PCA, tSNE, UMAP) and statistical evaluation of differential expression.
Main Results:
- Chevreul enables comprehensive processing and visualization of scRNA-seq data through user-friendly functions.
- The package supports full-length RNA sequencing data analysis, including specialized tools for isoform-level analysis and alternative splicing detection.
- Interactive visualization in the Shiny app allows dynamic exploration of gene expression and differential expression analysis without extensive programming.
Conclusions:
- Chevreul enhances scRNA-seq data analysis by offering ease of use, advanced isoform analysis, and robust visualization capabilities.
- The tool democratizes the analysis of full-length scRNA-seq data, particularly for researchers lacking extensive bioinformatics programming experience.
- Chevreul represents a valuable addition to the R Bioconductor ecosystem for single-cell genomics research.
