Package: VALERIE
Title: Visualising Splicing at Single-Cell Resolution
Version: 1.0.0
Description: 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>.
Imports: 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), scales (>= 1.0.0)
Encoding: UTF-8
Author: Sean Wen
Maintainer: Sean Wen <sean.wenwx@gmail.com>
License: GPL-3
RoxygenNote: 7.0.2
Suggests: knitr, rmarkdown
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
Built: R 4.0.0; ; 2020-02-27 15:19:04 UTC; windows
