The goal of scCity is to streamline the process of conducting single-cell analyses on the City of Hope High-Performance Computing (HPC) infrastructure. By leveraging the hprcc
package (https://github.com/cohmathonc/hprcc/), scCity abstracts the complexities involved in a typical single-cell analysis, enabling researchers to quickly and efficiently begin their work. The package integrates seamlessly with the R/Bioconductor container environment, as detailed here (https://github.com/drejom/vscode-rbioc), facilitating a smooth workflow for users of the City of Hope HPC.
To install the development version of scCity, use the following command:
remotes::install_github("drejom/scCity")
Please note, the remotes package is required for this installation method. If you do not have remotes installed, you can install it first using install.packages("remotes").
This is a basic example which shows you how to solve a common problem:
library(scCity)
## basic example code