VALERIE: Visualising Splicing at Single-Cell Resolution
Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events. PSI is the proportion of sequencing reads supporting the included exon/intron as defined by Shiozawa (2018) <doi:10.1038/s41467-018-06063-x>. PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) <doi:10.1371/journal.pcbi.1003118>. Computed PSI for each single cell are subsequently presented in the form of a heatmap implemented using the 'pheatmap' package by Kolde (2010) <https://CRAN.R-project.org/package=pheatmap>. Board overview of the mean PSI difference and associated p-values across different user-defined groups of single cells are presented in the form of a line graph using the 'ggplot2' package by Wickham (2007) <https://CRAN.R-project.org/package=ggplot2>.
||GenomicAlignments (≥ 1.16.0), GenomicRanges (≥ 1.32.0), IRanges (≥ 2.14.0), Rsamtools (≥ 1.34.0), plyr (≥ 1.8.4), ggplot2 (≥ 3.0.0), pheatmap (≥ 1.0.10), ggplotify (≥ 0.0.3), ggpubr (≥ 0.2.4), scales (≥ 1.0.0)
||Sean Wen <sean.wenwx at gmail.com>
Please use the canonical form
to link to this page.