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doc: add a section on related packages
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js2264 committed Jan 9, 2024
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Expand Up @@ -59,3 +59,23 @@ CoverageExperiment(tracks, GRanges("II:450001-455000"), width = 5000) |>
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![](man/figures/cov.png)

## Related projects

A number of `CRAN`, `Bioconductor` or `GitHub` packages already exist to enable genomic track
data visualization, for instance:

- `Gviz` [\[Bioconductor\]](https://www.bioconductor.org/packages/release/bioc/html/Gviz.html)
- `soGGi` [\[Bioconductor\]](https://www.bioconductor.org/packages/release/bioc/html/soGGi.html)
- `GenomicPlot` [\[Bioconductor\]](https://www.bioconductor.org/packages/release/bioc/html/GenomicPlot.html)
- `plotgardener` [\[Bioconductor\]](https://www.bioconductor.org/packages/release/bioc/html/plotgardener.html)
- `genomation` [\[Bioconductor\]](https://www.bioconductor.org/packages/release/bioc/html/genomation.html)
- `ggcoverage` [\[GitHub\]](https://github.com/showteeth/ggcoverage)
- `GenomicScores` [\[Bioconductor\]](https://www.bioconductor.org/packages/release/bioc/html/GenomicScores.html)

Compared to these existing solutions, `tidyCoverage` directly extends `SummarizedExperiment` infrastructure and
follows [tidy "omics" principles](https://www.biorxiv.org/content/10.1101/2023.09.10.557072v2). It does
not directly provide **plotting** functionalities, but instead focuses on data recovery, structure and coercion,
using a familiar grammar and standard representation of the data.
This ensures seamless integration of genomic track investigation in exisiting
`Bioconductor` and data analysis workflows.

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