https://github.com/dpeerlab/progressive-plasticity-crc-metastasis
Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"
https://github.com/dpeerlab/progressive-plasticity-crc-metastasis
Last synced: 6 months ago
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Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"
- Host: GitHub
- URL: https://github.com/dpeerlab/progressive-plasticity-crc-metastasis
- Owner: dpeerlab
- Created: 2024-05-22T21:56:45.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-12-01T20:21:52.000Z (over 1 year ago)
- Last Synced: 2024-12-01T21:26:25.744Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 2.11 MB
- Stars: 8
- Watchers: 2
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# Progressive Plasticity in Colorectal Cancer Metastasis
This repository accompanies the study *"Progressive Plasticity During Colorectal Cancer Metastasis"* published in *Nature* (available [here](https://www.nature.com/articles/s41586-024-08150-0)), aiming to reproduce key figures and analyses from the paper.
### Project Overview
The study investigates the progressive plasticity of cellular states during the metastasis of colorectal cancer. Using single-cell RNA sequencing data from primary tumors and metastases, we uncover dynamic cellular state transitions, highlighting specific lineage and state shifts associated with metastatic progression.
### Repository Structure
- **data/**: Contains required data files:
- **h5ads/**: AnnData files, such as `Tumor.h5ad`, `Epithelial.h5ad`, etc.
- **tables/**: Supplementary tables in `.xlsx` format.
- **other/**: Additional annotation and enrichment files.
- **notebooks/**: Jupyter notebooks for data download, preprocessing, and reproducing figures:
- `download_data.ipynb`: Guide for downloading data directly from AWS S3.
- `Figure_X.ipynb`: Notebooks for reproducing figures in the paper.
- **src/**: Source code modules organized by functionality, including utilities for data preprocessing (`pp`), plotting (`pl`), and label transfer or state analysis (`tl`).
### Data Access
The processed H5AD data for reproducing this analysis is hosted on AWS S3 at:
```
s3://dp-lab-data-public/progressive-plasticity-crc-metastasis
```
You can download H5ADs directly using the following links:
```
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/All.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Epithelial.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_Organoids.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_Tumor.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_Tumor_Mapping_Reference.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_shPROX1_Knockdown.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG150_Tumor.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG182_Tumor.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG183_Tumor.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Non-Tumor_Epithelial.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Tumor.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Untreated_Epithelial.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Wang_etal_Tumor.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Wang_etal_s1231_Tumor.h5ad
```
Additionally, all data is available vis a single download link in .tar.gz format:
```
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/data.tar.gz
```
### Installation
To install the required dependencies, ensure you have Python 3.8 or higher and use the `pyproject.toml`:
```bash
pip install .
```
For specific package versions, review the `pyproject.toml`.
### Quickstart
1. **Download Data**: Start with `download_data.ipynb` to load data files from AWS.
2. **Run Notebooks**: Open notebooks in the `notebooks` directory to generate individual figures.
---
This README provides a basic overview of the repository's contents and is designed to support the reproducibility of key analyses and findings from the paper.