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preamble.qmd
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preamble.qmd
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---
reference-section-title: References
bibliography: bibliography.bib
---
# Preamble {-}
Hi-C is an experimental method to quantify spatial interactions between any pair of genomic loci. While a number of command-line interfaces (CLI) exist to process and manipulate Hi-C data (e.g. `cooler` (@Abdennur2020Jan), `juicer` (@Durand2016Jul) and HiC-Pro (@Servant2015Dec)), they generally suffer from several limitations often found in emerging genomics techniques:
- **No genomic representation of Hi-C processed data**: the existing CLIs can efficiently parse Hi-C data as a numerical matrix and perform a few standard quantitative operations (e.g. contact matrix binning and normalization, dimensionality reduction, etc). However, they systematically fail to **represent a Hi-C contact matrix as a genomic object**. Qualitative analyses (e.g. intersecting chromatin loops with genomic features, finding genes overlapping with domains, etc) therefore remain extremely tedious.
- **No format-agnostic analysis libraries**. Three competing file format standards (`.(m)cool`, `.hic` and `HiC-Pro` files) currently exist to store Hi-C processed data and dedicated CLIs propose sets of tools specifically working with their corresponding Hi-C processed data file format. This has curbed the development of generic Hi-C data analysis libraries by favoring the emergence of several redundant tools.
- **Lack of integration within a biology-oriented community**. While rapid development of Hi-C analysis methodology is ongoing, it is primarily driven by small-scale teams rather than by a community as a whole. This oriented development is less likely to fulfill the needs met by other investigators.
In this book, we provide an **overview of a set of tools that enable processing, visualization and in-depth investigation of Hi-C data in R, ensuring intuitive integration of Hi-C data in the existing Bioconductor ecosystem**. We introduce a high-level `HiCExperiment` data structure to represent Hi-C data, directly extending robust, pre-existing core genomic classes offered by `Bioconductor`. This guarantees a stable and intuitive Hi-C data representation in R as a genomic entity, which is highly interoperable and can be used by all existing analysis packages in R.
On top of the `HiCExperiment` data structure, the `HiContacts` package offers extended functionalities to perform matrix-centric and interaction-centric analysis directly on `HiCExperiment` objects and provides powerful visualization tools specifically designed for Hi-C data to facilitate exploratory data analysis. In addition, the `HiCool` package implements a processing workflow based on a lightweight library to process raw Hi-C data into binned Hi-C contact matrices ready to be imported as `HiCExperiment` objects. Finally, the `fourDNData` and `DNAZooData` packages offer a gateway to major public data repositories directly in R.
# Package status {-}
|Github repo 💾|Doc 📘|Github checks ✅|Bioc builds 🏗|Lifecycle 🌱|
|--|--|--|--|--|
|[HiCExperiment](https://github.com/js2264/HiCExperiment)|[Doc](https://js2264.github.io/HiCExperiment)|[](https://github.com/js2264/HiCExperiment/actions/workflows/rworkflows.yml)|Bioc release:<br/>[](https://bioconductor.org/checkResults/release/bioc-LATEST/HiCExperiment/) <br/>Bioc devel:<br/>[](https://bioconductor.org/checkResults/devel/bioc-LATEST/HiCExperiment/)|[](https://www.tidyverse.org/lifecycle/#maturing)|
|[HiContacts](https://github.com/js2264/HiContacts)|[Doc](https://js2264.github.io/HiContacts)|[](https://github.com/js2264/HiContacts/actions/workflows/rworkflows.yml)|Bioc release:<br/>[](https://bioconductor.org/checkResults/release/bioc-LATEST/HiContacts/) <br/>Bioc devel:<br/>[](https://bioconductor.org/checkResults/devel/bioc-LATEST/HiContacts/)|[](https://www.tidyverse.org/lifecycle/#maturing)|
|[HiCool](https://github.com/js2264/HiCool)|[Doc](https://js2264.github.io/HiCool)|[](https://github.com/js2264/HiCool/actions/workflows/rworkflows.yml)|Bioc release:<br/>[](https://bioconductor.org/checkResults/release/bioc-LATEST/HiCool/) <br/>Bioc devel:<br/>[](https://bioconductor.org/checkResults/devel/bioc-LATEST/HiCool/)|[](https://www.tidyverse.org/lifecycle/#maturing)|
|[HiContactsData](https://github.com/js2264/HiContactsData)|[Doc](https://js2264.github.io/HiContactsData)|[](https://github.com/js2264/HiContactsData/actions/workflows/check-bioc.yml)|Bioc release:<br/>[](https://bioconductor.org/checkResults/release/data-experiment-LATEST/HiContactsData/) <br/>Bioc devel:<br/>[](https://bioconductor.org/checkResults/devel/data-experiment-LATEST/HiContactsData/)|[](https://lifecycle.r-lib.org/articles/stages.html#stable)|
|[DNAZooData](https://github.com/js2264/DNAZooData)|[Doc](https://js2264.github.io/DNAZooData)|[](https://github.com/js2264/DNAZooData/actions/workflows/rworkflows.yml)|Bioc release:<br/>[](https://bioconductor.org/checkResults/release/data-experiment-LATEST/DNAZooData/) <br/>Bioc devel:<br/>[](https://bioconductor.org/checkResults/devel/data-experiment-LATEST/DNAZooData/)|[](https://lifecycle.r-lib.org/articles/stages.html#stable)|
|[fourDNData](https://github.com/js2264/fourDNData)|[Doc](https://js2264.github.io/fourDNData)|[](https://github.com/js2264/fourDNData/actions/workflows/rworkflows.yml)|Bioc release:<br/>[](https://bioconductor.org/checkResults/release/data-experiment-LATEST/fourDNData/) <br/>Bioc devel:<br/>[](https://bioconductor.org/checkResults/devel/data-experiment-LATEST/fourDNData/)|[](https://lifecycle.r-lib.org/articles/stages.html#stable)|