VALERIE v1.0.0

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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>.

Readme

VALERIE (Visualising ALternative splicing Events from single-cell RIbonucleic-acid sequencing Experiments) is an R package for visualizing alternative splicing events at single-cell resolution. It allows visualisation of skipped-exon (SE), mutually exclusive exons (MXE), retained-intron (RI), alternative 5' splice site (A5SS), and alternative 3' splice site (A3SS) splicing events. The main feature that makes VALERIE suitable for visualising splicing events at single-cell resolution is the presentation of splicing events as percent spliced-in (PSI) values in the form of heatmap. This allows visualisation of splicing events of hundreds or even thousands of samples typical of single-cell experiments. Furthermore, it allows overall comparison of splicing events across user-defined groups of single cells, e.g. control vs. treatment. To demonstrate the utility of VALERIE, we visualised PKM gene MXE splicing events in 63 induced pluripotent stem cells (iPSCs), 69 motor neuron cells (MNs), and 73 neural progenitor cells (NPCs) from Song et al (Mol Cell, 2018). Here, it is evident from VALERIE that PKM is differentially spliced as iPSCs differentiate into either MNs or NPCs (Figure C below). As a comparison, coverage presentation of bulk samples (Figure A) and selected number of single cells (Figure B) are shown. In summary, compared to current genome browsers, VALERIE is able to capture cell-to-cell heterogeneity in splicing events in large number of single cells.

Functions in VALERIE

Name Description
PlotPSI.RI.TwoGroups Percent spliced-in (PSI) visualization for retained introns (RI)
PlotPSI.A5SS.TwoGroups Percent spliced-in (PSI) visualization for alternative 5' splice sites (A5SS)
PlotPSI.SE.MultiGroups Percent spliced-in (PSI) visualization for skipped exons (SE)
PlotPSI.MXE.MultiGroups Percent spliced-in (PSI) visualization for mutually exclusive exons (MXE)
ComputePSI Percent spliced-in (PSI) computation
PlotPSI.SE.TwoGroups Percent spliced-in (PSI) visualization for skipped exons (SE)
PlotPSI.A3SS.MultiGroups Percent spliced in (PSI) visualization for alternative 3' splice sites (A3SS)
PlotPSI.A3SS.TwoGroups Percent spliced in (PSI) visualization for alternative 3' splice sites (A3SS)
PlotPSI.A5SS.MultiGroups Percent spliced-in (PSI) visualization for alternative 5' splice sites (A5SS)
PlotPSI.MXE.TwoGroups Percent spliced-in (PSI) visualization for mutually exclusive exons (MXE)
PlotPSI.RI.MultiGroups Percent spliced-in (PSI) visualization for retained introns (RI)
PlotPSI Percent spliced-in (PSI) visualization for alternative splicing events
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Encoding UTF-8
License GPL-3
RoxygenNote 7.0.2
VignetteBuilder knitr
ByteCompile true
NeedsCompilation no
Packaged 2020-02-03 03:19:57 UTC; seanwenweixiong
Repository CRAN
Date/Publication 2020-02-11 10:40:05 UTC

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