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) . PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) . 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>.


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install.packages("VALERIE")

1.0.0 by Sean Wen, 5 months ago


Browse source code at https://github.com/cran/VALERIE


Authors: Sean Wen


Documentation:   PDF Manual  


GPL-3 license


Imports GenomicAlignments, GenomicRanges, IRanges, Rsamtools, plyr, ggplot2, pheatmap, ggplotify, ggpubr, scales

Suggests knitr, rmarkdown


See at CRAN