Package: VALERIE
Title: Visualising Splicing at Single-Cell Resolution
Version: 1.1.0
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 (>= 0.2.4), 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: 2026-06-15 09:29:43 UTC; root
Config/pak/sysreqs: libbz2-dev liblzma-dev xz-utils zlib1g-dev
Repository: https://cran.r-universe.dev
Date/Publication: 2020-07-10 09:20:13 UTC
RemoteUrl: https://github.com/cran/VALERIE
RemoteRef: HEAD
RemoteSha: 1bdf7ed399add8af8367c18bef52f6662571be87