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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 |
| Reference manual: | VALERIE.pdf |
| Vignettes: |
VALERIE |
| 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 |
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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.