> For the complete documentation index, see [llms.txt](https://zhonglab.gitbook.io/3dgenome/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis/analytical-pipelines.md).

# 3.2.2 Analytical Pipelines

With feature-rich Hi-C analysis, from Raw data download and pre-processing, to visualization and understanding the topological relationship, comprehensive and user-friendly tools (various feature extraction may need many dependencies which could be annoying installation) are wanted. Although some tools are specialized in specific problem, others that integrate the whole pipeline will be introduced here.