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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>.

Version: 1.1.0
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)
Suggests: knitr, rmarkdown
Published: 2020-07-10
DOI: 10.32614/CRAN.package.VALERIE
Author: Sean Wen
Maintainer: Sean Wen <sean.wenwx at gmail.com>
License: GPL-3
NeedsCompilation: no
In views: Omics
CRAN checks: VALERIE results

Documentation:

Reference manual: VALERIE.pdf
Vignettes: VALERIE

Downloads:

Package source: VALERIE_1.1.0.tar.gz
Windows binaries: r-devel: VALERIE_1.1.0.zip, r-release: VALERIE_1.1.0.zip, r-oldrel: VALERIE_1.1.0.zip
macOS binaries: r-release (arm64): VALERIE_1.1.0.tgz, r-oldrel (arm64): VALERIE_1.1.0.tgz, r-release (x86_64): VALERIE_1.1.0.tgz, r-oldrel (x86_64): VALERIE_1.1.0.tgz
Old sources: VALERIE archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=VALERIE to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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