Installation

Installation via R

One can install scSpotlight from GitHub with devtools or from r-universe. We recommend to use pak instead of traditional way, as it’s much faster.

# Install scSpotlight in R:
install.packages('scSpotlight', repos = c('https://obenno.r-universe.dev', 'https://cloud.r-project.org'))

# install.packages('pak')
pak::repo_add(scSpotlight = "https://obenno.r-universe.dev")
pak::pkg_install("scSpotlight")

# install.packages("devtools")
devtools::install_github("obenno/scSpotlight@v0.0.3")

# install.packages("pak")
pak::pkg_install("obenno/scSpotlight@v0.0.3")

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 specific port (e.g. 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")'