The analysis code for single-cell RNA-seq analysis of DKK1 osteosarcoma

This repository contains code used to process single-cell RNA sequencing (scRNA-seq) data. Follow the steps below to set up your environment and recreate the analysis.

Setup Instructions

1. Prepare the data Directory

   • Inside the data folder, create a subdirectory called aligned_samples.
   • Download the Cell Ranger count matrices from Zenodo and place them into the aligned_samples directory.
   • Ensure that the folders F43N, F43R, OSw3, OSW4, OSW5, and OSW6 are placed directly in this directory.

2. Obtain the Normal Osteoblast Dataset

   • Follow the instructions in data/Tulane_data/README.md to download and prepare the normal osteoblast dataset.

3. Create the output Directory

   • Create a folder named output. All analysis outputs will be stored here.

Instructions

To run all the scripts, navigate to the script folder and execute the following command:

bash main_section.sh

All the required Python package versions for the analysis are listed in requirements.txt.