chevreulShiny 0.99.29
chevreulShinyR is an open-source statistical environment which can be easily modified
to enhance its functionality via packages. chevreulShiny is a R
package available via the Bioconductor repository
for packages. R can be installed on any operating system from
CRAN after which you can install
chevreulShiny by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("chevreulShiny")
The chevreulShiny package is designed for single-cell RNA sequencing
data. The functions included within this package are derived from other
packages that have implemented the infrastructure needed for RNA-seq data
processing and analysis. Packages that have been instrumental in the
development of chevreulShiny include,
Biocpkg("SummarizedExperiment") and Biocpkg("scater").
R and Bioconductor have a steep learning curve so it is critical to
learn where to ask for help. The
Bioconductor support site is the main
resource for getting help: remember to use the chevreulShiny tag and check
the older posts.
chevreulShinyThe chevreulShiny package contains functions to preprocess, cluster, visualize, and
perform other analyses on scRNA-seq data. It also contains a shiny app for easy
visualization and analysis of scRNA data.
chvereul uses SingelCellExperiment (SCE) object type
(from SingleCellExperiment)
to store expression and other metadata from single-cell experiments.
This package features functions capable of:
library("chevreulShiny")
# Load the data
data("small_example_dataset")chevreulShiny includes a shiny app for exploratory scRNA data analysis and visualization which can be accessed via
minimalChevreulApp(small_example_dataset)
Note: the SCE object must be pre-processed and integrated (if required) prior to building the shiny app.
The app is arranged into different sections each of which performs different function. More information about individual sections of the app is provided within the “shiny app” vignette.
R session information.
#> R Under development (unstable) (2025-02-19 r87757)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
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#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] chevreulShiny_0.99.29 chevreulPlot_0.99.34 chevreulProcess_0.99.27 scater_1.35.3
#> [5] ggplot2_3.5.1 scuttle_1.17.0 shinydashboard_0.7.2 shiny_1.10.0
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