Table of contents

1. Installing bngal
2. Command-line utility (bngal-cli)
3. R package only with CRAN

Installing bngal

Although bngal is released as a standalone R package and can be interactively used in an IDE such as RStudio, I strongly recommend running the command-line utility wrapper (bngal-cli) to simplify its use, especially for first-time users. bngal-cli is currently only tested on MacOS and Linux.

You can quickly install both the bngal R package and its command-line utility wrapper via the following instructions:

Command line utility (recommended)

There are two ways to install the command line utility: DockerHub or Singularity/Apptainer. I recommend using one of the images hosted on DockerHub (do note your chip architecture - discussed further below). An installation route is also available from Anaconda or CRAN.

Docker (and Singularity/Apptainer)

Multi-platform Docker images for BNGAL are maintained here. Supported architectures for each release version are noted in the table below.

Image Tag	Version	Architecture
mjsel/bngal:1.0.1	1.0.1	amd64 / arm64
mjsel/bngal:1.0.0	1.0.0	amd64 / arm64

bngal-cli is easily installable if you use Docker:

docker pull mjsel/bngal:1.0.1

Alternatively, you can pull the same image if you use Singularity/Apptainer:

apptainer pull docker://mjsel/bngal:1.0.1

Anaconda virtual environment

If you instead prefer to use conda, please follow the instructions as follows.

1. Install the appropriate Anaconda version for your operating system if you don’t have it already.
2. Clone the bngal-cli GitHub repository into your directory of choice (my-directory) and run the setup script in a bash or zsh shell session. This will install the bngal R package within a new conda environment called “bngal”:

cd my-directory
git clone https://github.com/mselensky/bngal-cli --branch v.1.0
cd bngal-cli
bash bngal-setup.sh

And that’s it! Sit tight and grab a coffee while bngal-cli installs. It may take a few minutes.

Once you successfully install and activate the bngal environment, you can remove the bngal-cli folder. When the bngal environment is active, you will have access to two bngal-cli functions:

bngal-cli functions

Function	Application
bngal-build-nets	Build network model(s) according to defined cutoffs
bngal-summarize-nets	Summarize and visualize network statistics from bngal-build-nets

R package only with CRAN

If you only want to use the bngal R package interactively, you can install it and its dependencies within an active R session via:

source("https://raw.githubusercontent.com/mselensky/bngal-cli/main/R/install-R-pkgs.R")

Please refer to the internal documentation when using the standalone R package.