ShinyCellModular

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ShinyCellModular is a modular version of ShinyCell developed at the Monash Genomics and Bioinformatics Platform (MGBP). Each module consists on a tab in the app. Each module is created individually and is it selfcontained. ShinyCellModular supports large scRNAseq and multimodal datasets with fast on-demand HDF5 access, extended visualisations, improved filtering, and publication-ready plots. Its modular structure makes it flexible, scalable, and easy to customise. Example of ShinyCellModular in Single Cell RNAseq

Review Docs for further information on functions details
Review Docs for further information on development instructions

Features

• Modular UI and server structure
• Supports scRNAseq, ATAC, and multimodal datasets
• Fast HDF5 on-demand loading
• Publication‑ready plots (PNG/PDF export)
• Extended visualisation tabs (UMAP, 3D UMAP, violin, bubble, heatmap, coexpression, AUC marker genes, pseudobulking)
• Cell subsetting and conditional plotting
• Easy integration with new modules via a registry system

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Fast usage just needs 3 steps

1. Setup

Clone this repository

git clone https://github.com/MonashBioinformaticsPlatform/ShinyCellModular.git

Open the .Rproj file

Load RENV - all require library

install.packages("renv")
renv::restore()

Run the 2 helper functions prepShinyCellModular() and useShinyCellModular()

2. prepShinyCellModular()

library(ShinyCell) #devtools::install_github("SGDDNB/ShinyCell")
library(Seurat)
library(Signac)
library(dplyr)


# Prepare seurat object, checks Key names, creates sc1counts.h5, adds a 3D reduction UMAP
cnts<-LoadSeuratRds("seurat_object.Rds")

source("functions/prepShinyCellModular.R")

prepShinyCellModular(seurat_rds = "seurat_object.rds",
                  out_dir = "testing_data_RNA", 
                  assays_selected = "RNA",
                  do_umap3d = TRUE,  
                  do_markers= TRUE,   
                  markers_res_pattern = "wsnn_res",
                  )

3.useShinyCellModular()

# Create a new app.R with the modified ShinyCell tabs

source("functions/useShinyCellModular.R")

useShinyCellModular(
    shiny.dir="testing_data/",
    shinycellmodular.dir.src="~/ShinyCellModular/",
    rsconnect.deploy = FALSE,
    data_type = "",
    enabled_tabs = c("cellinfo_cellinfo",
                    "cellinfo_geneexpr",
                    "cellinfo3D_cellinfo3D",
                    "cellinfo3D_geneexpr3D",
                    "genecoex",
                    "violin_boxplot",
                    "proportions",
                    "bubble_heatmap",
                    "pseudobulk"),
    overwrite_modules = TRUE,
    app_title='Testing'
)