{"id":37716720,"url":"https://github.com/dpeerlab/progressive-plasticity-crc-metastasis","last_synced_at":"2026-01-16T13:27:35.346Z","repository":{"id":260169399,"uuid":"804588013","full_name":"dpeerlab/progressive-plasticity-crc-metastasis","owner":"dpeerlab","description":"Notebooks for generating figures in \"Progressive Plasticity During Colorectal Cancer Metastasis\"","archived":false,"fork":false,"pushed_at":"2024-12-01T20:21:52.000Z","size":2208,"stargazers_count":8,"open_issues_count":1,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-12-01T21:26:25.744Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dpeerlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-05-22T21:56:45.000Z","updated_at":"2024-12-01T20:21:55.000Z","dependencies_parsed_at":"2024-12-01T21:22:41.241Z","dependency_job_id":"c16eaf82-15f1-4fc3-bee7-e5e98047362f","html_url":"https://github.com/dpeerlab/progressive-plasticity-crc-metastasis","commit_stats":null,"previous_names":["dpeerlab/progressive-plasticity-crc-metastasis"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dpeerlab/progressive-plasticity-crc-metastasis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dpeerlab%2Fprogressive-plasticity-crc-metastasis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dpeerlab%2Fprogressive-plasticity-crc-metastasis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dpeerlab%2Fprogressive-plasticity-crc-metastasis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dpeerlab%2Fprogressive-plasticity-crc-metastasis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dpeerlab","download_url":"https://codeload.github.com/dpeerlab/progressive-plasticity-crc-metastasis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dpeerlab%2Fprogressive-plasticity-crc-metastasis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28479033,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-16T13:27:35.271Z","updated_at":"2026-01-16T13:27:35.334Z","avatar_url":"https://github.com/dpeerlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Progressive Plasticity in Colorectal Cancer Metastasis\n\nThis 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.\n\n### Project Overview\nThe 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. \n\n### Repository Structure\n\n- **data/**: Contains required data files:\n  - **h5ads/**: AnnData files, such as `Tumor.h5ad`, `Epithelial.h5ad`, etc.\n  - **tables/**: Supplementary tables in `.xlsx` format.\n  - **other/**: Additional annotation and enrichment files.\n\n- **notebooks/**: Jupyter notebooks for data download, preprocessing, and reproducing figures:\n  - `download_data.ipynb`: Guide for downloading data directly from AWS S3.\n  - `Figure_X.ipynb`: Notebooks for reproducing figures in the paper.\n  \n- **src/**: Source code modules organized by functionality, including utilities for data preprocessing (`pp`), plotting (`pl`), and label transfer or state analysis (`tl`).\n\n### Data Access\nThe processed H5AD data for reproducing this analysis is hosted on AWS S3 at:\n```\ns3://dp-lab-data-public/progressive-plasticity-crc-metastasis\n```\nYou can download H5ADs directly using the following links:\n```\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/All.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Epithelial.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_Organoids.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_Tumor.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_Tumor_Mapping_Reference.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG146_shPROX1_Knockdown.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG150_Tumor.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG182_Tumor.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/KG183_Tumor.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Non-Tumor_Epithelial.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Tumor.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Untreated_Epithelial.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Wang_etal_Tumor.h5ad\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/h5ads/Wang_etal_s1231_Tumor.h5ad\n```\nAdditionally, all data is available vis a single download link in .tar.gz format:\n```\nhttps://dp-lab-data-public.s3.us-east-1.amazonaws.com/progressive-plasticity-crc-metastasis/data.tar.gz\n```\n\n### Installation\n\nTo install the required dependencies, ensure you have Python 3.8 or higher and use the `pyproject.toml`:\n```bash\npip install .\n```\n\nFor specific package versions, review the `pyproject.toml`.\n\n### Quickstart\n\n1. **Download Data**: Start with `download_data.ipynb` to load data files from AWS.\n2. **Run Notebooks**: Open notebooks in the `notebooks` directory to generate individual figures.\n\n---\n\nThis 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdpeerlab%2Fprogressive-plasticity-crc-metastasis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdpeerlab%2Fprogressive-plasticity-crc-metastasis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdpeerlab%2Fprogressive-plasticity-crc-metastasis/lists"}