RIF spatial transcriptomics with Nanostring GeoMX

Running the analysis

With singularity

1. Install Singularity

2. Build the singularity container:

    sudo singularity build runAnalysis.img Singularity

3. Run the analysis and render the html notebooks with a single command:

    ./runAnalysis.img

Alternatively using RScript

1. Install the needed R packages

    RScript install/install.R

2. Run the analysis and render the html notebooks

    RScript runAnalysis.R