CRAN/E | VALERIE

VALERIE

Visualising Splicing at Single-Cell Resolution

Installation

About

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) . 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) .

Key Metrics

Version 1.1.0
Published 2020-07-10 986 days ago
Needs compilation? no
License GPL-3
CRAN checks VALERIE results

Downloads

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Last 7 days 41 +37%
Last 30 days 125 -2%
Last 90 days 361 -23%
Last 365 days 1.922 -38%

Maintainer

Maintainer

Sean Wen

sean.wenwx@gmail.com

Authors

Sean Wen

Material

Reference manual
Package source

Vignettes

VALERIE

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

VALERIE archive

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