University of Oxford researchers present VALERIE (Visualising alternative splicing events from single-cell ribonucleic acid-sequencing experiments), an R package for visualising alternative splicing events at single-cell resolution. To explore any given specified genomic region, corresponding to an alternative splicing event, VALERIE generates an ensemble of informative plots to visualise cell-to-cell heterogeneity of alternative splicing profiles across single cells and performs statistical tests to compare percent spliced-in (PSI) values across the user-defined groups of cells. Among the features available, VALERIE displays PSI values, in lieu of read coverage, which is more suitable for representing alternative splicing profiles for a large number of samples typically generated by single-cell RNA-sequencing experiments.
Overview of VALERIE
(A) The workflow of data processing steps. VALERIE computes percent spliced-in (PSI) values from read coverage information and integrates alternative splicing coordinates and cell group annotations from exon and sample information files to generate heatmap of PSI, and line graphs of mean PSI and adjusted p-values at each nucleotide position. (B) The role of VALERIE in the overall process of identifying candidate alternative splicing events for downstream functional studies. VALERIE serves as a visual inspection and validation of alternative splicing events identified from genome-wide analysis such as differential analysis. In conjunction with, or as an alternative to, other technical validation approaches as such sc-qPCR, VALERIE can enable selection of candidate alternative splicing events for downstream functional validation. A3SS: Alternative 3’ splice site. A5SS: Alternative 5’ splice site. MXE: Mutually exclusive exons. RI: Retained-intron. sc-qPCR: Single-cell quantitative polymerase chain reaction. SE: Skipped-exon. smFISH: Single-molecule fluorescence in situ hybridisation.
Availability – VALERIE is available on the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/VALERIE/index.html.