scSpotlight

The goal of scSpotlight is to simplify your single cell analysis and easily annotate your dataset with curated cell type markers. scSpotlight is built on shiny, Seurat and regl-scatterplot. Please refer to the documentation website for detailed instructions:

• https://obenno.github.io/scSpotlight/
• https://scspotlight.netlify.app/ (EN, CN)

Installation

You can install the development version of scSpotlight from GitHub with:

# install.packages("devtools")
devtools::install_github("obenno/scSpotlight")

or a much faster installation with pak:

# install.packages("pak")
pak::pkg_install("obenno/scSpotlight")

Dependency policy (dev + CI)

• DESCRIPTION is the source of truth for package dependencies.
• renv.lock is used for reproducible project environments (for example pkgdown builds and deployment workflows).
• Commit renv.lock, renv/activate.R, and renv/settings.json.
• Do not commit renv/library/ or other cache directories.
• CI jobs can use both approaches: install from DESCRIPTION for package checks, and run renv::restore() for reproducible docs/app jobs.

Docker

To pull the latest image from the command line

docker pull registry-intl.cn-hangzhou.aliyuncs.com/thunderbio/scspotlight:0.0.3

To run the app on port:8081, please use the command below:

docker run -p 8081:8081 registry-intl.cn-hangzhou.aliyuncs.com/thunderbio/scspotlight:0.0.3 Rscript -e 'scSpotlight::run_app(options = list(port=8081, host="0.0.0.0", launch.browser = FALSE), runningMode="processing")'