Effects-of-a-humanized-CD47-antibody-and-recombinant-SIRPalpha-proteins-on-TNBC-stem-cells

This code accompanies the paper entitled: "Effects of a humanized CD47 antibody and recombinant SIRPalpha proteins on triple negative breast carcinoma stem cells" (CCBR-699)

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/Effects-of-a-humanized-CD47-antibody-and-recombinant-SIRPalpha-proteins-on-TNBC-stem-cells.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 Effects-of-a-humanized-CD47-antibody-and-recombinant-SIRPalpha-proteins-on-TNBC-stem-cells .

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 Effects-of-a-humanized-CD47-antibody-and-recombinant-SIRPalpha-proteins-on-TNBC-stem-cells

6. Run the following code.

   • cd /mnt
   • bash run_pipeline.sh

This repository is the location Josh will extract CCBR-699 to.

The final R3 extraction branch for this project is found here:

https://nidap.nih.gov/workspace/vector/view/ri.vector.main.workbook.19324ee7-7869-4b9e-88a4-2e77f2f41199?branch=Cg_and_Si_Co-Analysis_R3