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3D intercellular assembly of decellularized matrix recapitulates in vivo tumor heterogeneity

This code accompanies the paper entitled: "3D intercellular assembly of decellularized matrix recapitulates in vivo tumor heterogeneity." (CCBR-1223)

To reproduce these results, follow these steps:

  1. Clone this GitHub repo (i.e. the page you are on):

    • git clone https://github.com/NIDAP-Community/3D-intercellular-assembly-of-decellularized-matrix-recapitulates-in-vivo-tumor-heterogeneity.git

  2. The input files for this pipeline will be available upon request. Please reach out to the authors before continue to following steps

  3. Install docker and build the docker container:

    • Navigate to the cloned repository directory.
    • Move to the ./Docker_file/ directory of this repo

  4. Build the container:

    • docker build --tag nidap-analysis-r3 .

  5. Navidate to the cloned repository directory, Run the conainer by mounting the ./src/ directory of the repo to /tmp/ in the container:

    • docker run -ti -v $(pwd)/src:/mnt nidap-analysis-r3

  6. Run the following code.

    • cd /mnt
    • bash run_pipeline.sh