paulsengroup/stripepy

StripePy

本仓库托管__StripePy__的Docker镜像：这是一个使用几何推理识别3C和Hi-C接触图中架构条纹的工具。

快速参考

StripePy由https://github.com/paulsengroup开发和维护。

如果您对StripePy有疑问，请在GitHub上发起新的https://github.com/paulsengroup/stripepy/discussions。

有用链接

• 代码仓库：https://github.com/paulsengroup/StripePy
• 文档：https://github.com/paulsengroup/StripePy?tab=readme-ov-file#stripepy
• Dockerfile：https://github.com/paulsengroup/StripePy/blob/main/Dockerfile

额外信息

每当主分支有提交推送或新发布被标记时，镜像会通过GitHub Actions自动构建。

构建日志：https://github.com/paulsengroup/StripePy/actions/workflows/build-dockerfile.yml

支持的标签和Dockerfile链接

• https://hub.docker.com/r/paulsengroup/stripepy/tags?name=main - https://github.com/paulsengroup/StripePy/blob/main/Dockerfile
• https://hub.docker.com/r/paulsengroup/stripepy/tags?name=1.3.0 - https://github.com/paulsengroup/StripePy/blob/v1.3.0/Dockerfile
• https://hub.docker.com/r/paulsengroup/stripepy/tags?name=0.0.2 - https://github.com/paulsengroup/StripePy/blob/v0.0.2/Dockerfile

镜像内容

此镜像包含StripePy库的CLI工具。CLI由单个可执行文件（stripepy）和几个子命令组成。

快速入门

首先，从DockerHub拉取最新版本的StripePy。

对于生产环境，建议拉取最新稳定版本：

bash
docker pull docker.xuanyuan.run/paulsengroup/stripepy:1.3.0

其他情况可拉取最新可用镜像：

bash
docker pull docker.xuanyuan.run/paulsengroup/stripepy

注意：根据操作系统不同，您可能需要管理员/root权限（通常通过在拉取命令前添加sudo获得）。

打印帮助信息

console
user@dev:/tmp$ docker run paulsengroup/stripepy --help

usage: stripepy [-h] [-v] {call,download,plot,view} ...

stripepy旨在通过几何推理（包括拓扑持久性和拟插值）识别接触图（.hic、.mcool、.cool）中的线性模式。

选项:
  -h, --help            显示此帮助消息并退出
  -v, --version         显示程序版本号并退出

子命令:
  {call,download,plot,view}
                        可用子命令列表:
    call                stripepy按四个连续步骤工作:
                        • 步骤1: 预处理
                        • 步骤2: 感兴趣位点（也称为"种子"）的识别
                        • 步骤3: 形状分析（即宽度和高度估计）
                        • 步骤4: 信号分析
    download            简化下载可用于测试StripePy的数据集的辅助命令。
    plot                生成各种静态图，用于可视化检查stripepy call产生的输出。
    view                从stripepy call生成的HDF5文件中获取条纹数据。

有关如何使用stripepy的更多详细信息和示例，请参考官方https://github.com/paulsengroup/StripePy?tab=readme-ov-file#stripepy。

引用

如果您在研究中使用StripePy，请引用以下文献：

Andrea Raffo, Roberto Rossini, Jonas Paulsen, StripePy: fast and robust characterization of architectural stripes bioRxiv 2024.12.20.629789; doi: https://doi.org/10.1101/2024.12.20.629789

bibtex
@article {stripepy,
  author = {Raffo, Andrea and Rossini, Roberto and Paulsen, Jonas},
  title = {StripePy: fast and robust characterization of architectural stripes},
  elocation-id = {2024.12.20.629789},
  year = {2024},
  doi = {10.1101/2024.12.20.629789},
  publisher = {Cold Spring Harbor Laboratory},
  abstract = {
    Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair.
    Despite their importance, few tools exist for automatic stripe detection.
    We introduce StripePy, which leverages computational geometry methods to identify and analyze architectural stripes in contact maps from Chromosome Conformation Capture experiments like Hi-C and Micro-C.
    StripePy outperforms existing tools, as shown through tests on various datasets and a newly developed simulated benchmark, StripeBench, providing a valuable resource for the community.Competing Interest StatementThe authors have declared no competing interest.@
  },
  URL = {https://www.biorxiv.org/content/early/2024/12/22/2024.12.20.629789},
  eprint = {https://www.biorxiv.org/content/early/2024/12/22/2024.12.20.629789.full.pdf},
  journal = {bioRxiv}
}