Installation

Here we provide open source code of sc2MeNetDrug in GitHub.

Requirements

1. Typically, sc2MeNetDrug may require a substantial amount of memory when processing large scRNA-seq datasets. Given the typical size of scRNA-seq data, we recommend using a computing resource with at least 16GB of RAM (32GB or more is highly recommended).
2. R environment with R>= 4.2.1.
3. RStudio or other applications that can deploy R Shiny apps.

4. All denpendences R packages:

   shinydashboard
   shiny
   shinyjs
   shinyBS
   plotly
   r2d3
   DT
   stringr
   shinyFiles
   fs
   data.table
   org.Hs.eg.db
   GO.db
   GOSemSim
   jsonlite
   dplyr
   Seurat
   SeuratWrappers
   igraph
   rcdk
   fingerprint
   glmGamPoi
   

5. If you are in a Mac environment, you may need environment that can compile c++ packages. You can install that by entering the following script in the terminal:

   xcode-select --install

Instruction for the installation

1. In your terminal, cd to your desired directory and clone the source code by: git clone https://github.com/fuhaililab/sc2MeNetDrug.git

2. Open the source code in RStudio and run the dependencies.R script to install all dependent packages used in sc2MeNetDrug (ignore this step if you already have all packages installed).

3. Go to R directory and open ui.R or server.R in Rstudio, you will see Run App in the top right of the interface, click it to open the sc2MeNetDrug.