# Orchestrating Hi-C analysis with Bioconductor

> The primary aim of this book is to introduce the R user to Hi-C analysis. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents Bioconductor tools that can be leveraged to process, analyze, explore and visualize Hi-C data.

<!-- biocbook:start -->
- Book package: `OHCA` 1.9.4 (Bioconductor 3.24), source: <https://github.com/js2264/OHCA>
- Install: `BiocManager::install("OHCA")` (Bioconductor) or `BiocManager::install("js2264/OHCA")` (GitHub)
- Docker image with every dependency: `docker run -it ghcr.io/js2264/ohca:1.9.4 R`
- Python environment (conda): `python=3.12`, `pip`; from PyPI: `cooler==0.10.4`, `cooltools==0.7.1`, `bioframe==0.8.0`, `pandas==2.3.3`, `matplotlib==3.11.2`, provisioned by `BiocBook::setup_python()` from `inst/requirements.yml`
- Other versions of this book: one per Bioconductor release, at `https://js2264.github.io/OHCA/<version>/` (e.g. <https://js2264.github.io/OHCA/devel/>), indexed in <https://js2264.github.io/OHCA/llms.txt>
<!-- biocbook:end -->

## Chapters

- [Orchestrating Hi-C analysis with Bioconductor](index.html)
- [Preamble](pages/preamble.html)
- Fundamentals concepts
  - [Hi-C pre-processing steps](pages/principles.html)
  - [Hi-C data structures in R](pages/data-representation.html)
  - [Manipulating Hi-C data in R](pages/parsing.html)
  - [Hi-C data visualization](pages/visualization.html)
- In-depth Hi-C analysis
  - [Matrix-centric analysis](pages/matrix-centric.html)
  - [Interactions-centric analysis](pages/interactions-centric.html)
  - [Finding topological features in Hi-C](pages/topological-features.html)
- Advanced Hi-C topics
  - [Data gateways: accessing public Hi-C data portals](pages/disseminating.html)
  - [Interoperability: using HiCExperiment with other R packages](pages/interoperability.html)
  - [Interoperability with `python`: `cooltools`](pages/interoperability-python.html)
  - [Workflow 1: Distance-dependent interactions across yeast mutants](pages/workflow-yeast.html)
  - [Workflow 2: Chromosome compartment cohesion upon mitosis entry](pages/workflow-chicken.html)
  - [Workflow 3: Inter-centromere interactions in yeast](pages/workflow-centros.html)
