easyshiny

easyshiny is a R package to quickly create an interactive web application to visualise and explore single-cell data.

Installation

Run the following code to check if the dependency packages are installed, else install them if required:

pkgs = c("bslib", "data.table", "DT", "ggdendro", "ggplot2", "ggplotify", "ggrepel", "glue", "grid", "hdf5r", "magrittr", "Matrix", "patchwork", "RColorBrewer", "readr", "remotes", "reticulate", "Seurat", "shiny", "shinycssloaders", "shinyhelper")

pkg = pkgs[!(pkgs %in% installed.packages()[,"Package"])]
if(length(pkg)){install.packages(pkg)}

# optional if you want to use custom fonts
install.packages("showtext")
 
# If you are using h5ad file as input, run the code below as well
# reticulate::py_install("anndata")

easyshiny can then be installed from GitHub as follows:

remotes::install_github("NBISweden/easyshiny")

For usage and deploy guide, see here.

Screenshots

Single dataset

Multiple datasets

Cell information vs gene expression.

Cell information vs cell information.

Gene expression vs gene expression.

Gene co-expression.

Proportion plot.

Heatmap/Dotplot/Bubble plot.

Violin plot.

Acknowledgements

easyshiny is built on ShinyCell.

Ouyang, J. F., Kamaraj, U. S., Cao, E. Y., & Rackham, O. J. (2021). ShinyCell: simple and sharable visualization of single-cell gene expression data. Bioinformatics, 37(19), 3374-3376.

easyshiny was developed in collaboration with Makinen Lab. Thanks to Taija Mäkinen and Marle Kraft for their valuable contribution.

Issues

Report issues here.

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2023 • NBIS