# 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. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://zhonglab.gitbook.io/3dgenome/chapter2-computational-analysis/3.2-higer-order-data-analysis/analytical-pipelines.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.