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cite MGnifyR with notebook references (#594)
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Signed-off-by: Daena Rys <[email protected]>
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Daenarys8 authored Aug 6, 2024
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Expand Up @@ -121,9 +121,11 @@ The following DA methods support `(Tree)SummarizedExperiment`.
- [ALDEx2](https://www.bioconductor.org/packages/release/bioc/html/ALDEx2.html) for differential abundance analysis

### Other relevant packages

- [LinDA](https://github.com/zhouhj1994/LinDA)
- [vegan](https://vegandevs.github.io/vegan/)
- [MGnifyR](https://github.com/EBI-Metagenomics/MGnifyR) for accessing and processing MGnify data in R
- [MGnify Notebooks](https://docs.mgnify.org/src/notebooks_list.html)
- [EMBL-EBI MGnify user guides and resources](https://github.com/EBI-Metagenomics/notebooks)
- [LinDA](https://github.com/zhouhj1994/LinDA) for differential abundance analysis
- [vegan](https://vegandevs.github.io/vegan/) for community ecologists
- [philr](http://bioconductor.org/packages/devel/bioc/html/philr.html) (@Silverman2017) phylogeny-aware phILR transformation
- [MicrobiotaProcess](https://bioconductor.org/packages/release/bioc/html/MicrobiotaProcess.html) for the "tidy" analysis of microbiome and other ecological data
- [Tools for Microbiome Analysis](https://microsud.github.io/Tools-Microbiome-Analysis/)
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