Shiny App for our 2025 manuscript, Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1S858R Schinzel-Giedion Syndrome patient variant mouse

Repo for shiny app: https://lasseignelab.shinyapps.io/setbp1_as/ 

./MARVEL/

• Script_DROPLET_07_ADHOC_PLOT_PCA_2_PlotValues_PSI.R - A script from the MARVEL package that needed more memory efficiency.

• Script_DROPLET_07_ADHOC_PLOT_PCA_3_PlotValues_Gene.R - A script from the MARVEL package that needed a bug fixed.  Also, modifications were needed to make memory usage more efficient.

./R/

• data.R - A script that transforms processed data related to the manuscript into files that will be more memory efficient in the Shiny app.

• external_link.R - A script that defines the function external_link(href, text).  This function creates links to external sites that open in a new browser tab.

• gene_expression_plot_image.R - A script that defines the function gene_expression_plot_image(data_file, data_name, gene).  This function creates a PNG image of a gene expression plot in a way that makes memory usage more efficient.

• gene_position.R - A script that defines the function gene_position(setbp1_metadata, gene).  This function uses splice junction metadata to calculate the DNA position of a gene.

• genome_browser_links.R - A script that defines the function genome_browser_links(setbp1_metadata, gene).   This function creates browser links to the UCSC Genome Browser and Ensembl Genome Browser for a gene.

• ggplot_theme.R - A script that defines the function ggplot_theme().  This function defines a shared ggplot theme used in almost all plots.

• initialize_last_plot_click.R - A script that defines the function initialize_last_plot_click(session).  This function initializes a session variable to keep up with the last time the plot button was clicked.

• initiate_gene_expression_plot.R - A script that defines the function initiate_gene_expression_plot(session, plot_click, plot_type).  This function determines whether all the selections for a gene expression plot have been selected before the plot button is clicked.  If so, the plot is initiated by returning a value other than NULL.

• initate_splice_junction_plot.R - A script that defines the function initiate_splice_junction_plot(session, plot_click, plot_type).  This function determines whether all the selections for a splice junction plot have been selected before the plot button is clicked.  If so, the plot is initiated by returning a value other than NULL.

• plot.R - A script that pre-renders the cell types UMAP plot.  This plot stays the same, needs to be created faster, and uses too much memory.  Pre-rendering solves all these problems.

• splice_junction_plot_image.R - A script that defines the function splice_junction_plot_image (data_file, data_name, tissue, splice_junction). This function renders splice junction plots while minimizing memory usage.

./bin/container/

• .gitignore: A file that informs git which files or file patterns to ignore. 

• Dockerfile: A file that includes all packages and libraries included in the Docker image of this repository.

• start-container.sh: A bash script that provides code to acquire and execute the Docker image using Singularity.

./data/

• .gitignore: A file that informs git which files or file patterns to ignore. 

• Instructions for generating Shiny app data files can be found in the ./R/data.R script.

./original_data/

• .gitignore: A file that informs git which files or file patterns to ignore. 

• The data files required to create the Shiny app data are included in the processed data Zenodo repository of our manuscript.

./www/

• brain_cell_types.png - Pre-rendered cell type UMAP plot for the cerebral cortex.

• favicon.ico - Lasseigne lab logo for the README

• kidney_cell_types.png - Pre-rendered cell type UMAP plot for the kidney.

• Logo_only.png - Lab logo for the Shiny app footer

• setbp1.png - Graphical abstract from the manuscript.

• sj_usage.png - Graphic explaining splice junction usage calculation.

• styles.css - Cascading style sheet for the application.

.gitignore - The purpose of this file is to prevent unnecessary files from being added to the GitHub Repo.

.rscignore - The purpose of this file is to prevent unnecessary files from being deployed with the Shiny application.

.rsconnect_profile - A script that includes information used by the rsconnect R package. 

.LICENSE - A text file that includes the MIT License information of this GitHub repository.

README.md - A plain text file that contains project information portrayed in the GitHub repository’s README.

Setbp1_Alternative_Splicing_Shiny_App.Rproj - A file created by RStudio that contains project-specific settings.

app.R - A script that starts the Shiny application.

server.R - A script that defines the Shiny app server-side reactive functionality, which responds to the user’s interactions with the user interface.

shiny-run.R - A script to start the Shiny app in a console window.  This makes development quicker by automatically reloading the shiny app when files change.  Also, Shiny app tracing is output in the console to make debugging easier.

ui.R - A script that defines the Shiny app user interface (UI).

Release v2.0.0: Addition of kidney alternative splicing analyses

What's Changed

• Fix alternative splicing summaries by @toniecrumley in https://github.com/lasseignelab/Setbp1_Alternative_Splicing_Shiny/pull/2
• Update user interface content by @tsoelter in https://github.com/lasseignelab/Setbp1_Alternative_Splicing_Shiny/pull/4
• Review revisions by @toniecrumley in https://github.com/lasseignelab/Setbp1_Alternative_Splicing_Shiny/pull/3

New Contributors

• @tsoelter made their first contribution in https://github.com/lasseignelab/Setbp1_Alternative_Splicing_Shiny/pull/4

Full Changelog: https://github.com/lasseignelab/Setbp1_Alternative_Splicing_Shiny/compare/v1.0.0...v2.0.0