Gastric Cancer single-cell Explorer

Shiny app for exploring gastric cancer single-cell atlas objects plus lightweight Xenium spatial exports, precomputed marker tables, average-expression caches, and malignant-vs-normal quadrant DEG plots.

Runtime layout

The app is now runtime-configurable and does not require Mac-specific paths.

• Code directory: this repository
• Data directory: controlled by GC_APP_DATA_DIR
• Default local behavior: if GC_APP_DATA_DIR is unset, the app looks for data in ./data and then in the parent directory of the app

Required runtime files

Place the files from data directory mounted into the container (GCshinyapp_data folder):

• seurat_merged_TME_malignant_final_umap_app_slim.rds
• seurat_epithelial_normal_final_final_app_slim.rds
• seurat_cancercells_final_app_slim.rds
• seurat_Stromal_final_app_slim.rds
• seurat_CD8T_final2_app_slim.rds
• seurat_CD4T_final2_app_slim.rds
• seurat_B_final2_app_slim.rds
• seurat_Mye_final2_app_slim.rds
• *_avg_cache.rds files for the objects you want to support
• *_quadrant_cache.rds for quadrant DEG plots
• dataset_group_colors.rds
• path_group_colors.rds
• subcluster_ct_colors_combined.rds
• markers_RNA_merged_AllCelltypes_final.xlsx
• marker/DE .xlsx files for the other atlas objects you want exposed
• atlas_app_inputs/export_manifest.tsv
• atlas_app_inputs/<sample_id>/cells.rds
• atlas_app_inputs/<sample_id>/image_lowres.png
• atlas_app_inputs/<sample_id>/image_meta.rds
• atlas_app_inputs/<sample_id>/neighborhood_summary.rds
• atlas_app_inputs/<sample_id>/neighborhood_composition.rds
• atlas_app_inputs/<sample_id>/<sample_id>_counts_sce.rds if you want to rebuild Xenium marker assets
• atlas_app_inputs/<sample_id>/marker_expr/ if you want the Xenium Marker Overlay tab available immediately

Example shared host path used for this project:

• /mnt/ix1/Projects_lite/junhacha/GCshinyapp_data

Local run

cd /path/to/GC-atlas-explorer
GC_APP_DATA_DIR=/path/to/data R -e "shiny::runApp('.', launch.browser = TRUE)"

For the shared project storage, that becomes:

GC_APP_DATA_DIR=/mnt/ix1/Projects_lite/junhacha/GCshinyapp_data R -e "shiny::runApp('.', launch.browser = TRUE)"

Docker run

Build:

docker build -t gc-singlecell-explorer .

Run:

docker run --rm -p 3838:3838 \
  -e GC_APP_DATA_DIR=/data \
  -v /mnt/ix1/Projects_lite/junhacha/GCshinyapp_data:/data:ro \
  gc-singlecell-explorer

Then open:

• http://<server-host>:3838

Docker Compose

Example file is included at docker-compose.yml.

Set the host data path in .env:

cp .env.example .env

Then edit:

GC_APP_HOST_DATA_DIR=/mnt/ix1/Projects_lite/junhacha/GCshinyapp_data

Start:

docker compose up -d --build

Admin handoff

1. This repository
2. A host data directory containing the required .rds, cache, and .xlsx files
3. One of:
   • docker build + docker run
   • docker compose up -d --build

Updating the app later

You can keep extending the app after deployment. Update the code in this repo, rebuild the container, and restart it. The shared data directory can stay mounted in the same place.