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Add DAA methods (#647)
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TuomasBorman authored Dec 2, 2024
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14 changes: 14 additions & 0 deletions inst/assets/bibliography.bib
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Expand Up @@ -2307,3 +2307,17 @@ @Manual{Benedetti2024miadash
note = {R package version 0.99.0},
url = {https://github.com/microbiome/miaDash},
}

@article{mangiola2023,
author = {Stefano Mangiola and Alexandra J. Roth-Schulze and Marie Trussart and Enrique Zozaya-Valdés and Mengyao Ma and Zijie Gao and Alan F. Rubin and Terence P. Speed and Heejung Shim and Anthony T. Papenfuss },
title = {sccomp: Robust differential composition and variability analysis for single-cell data},
journal = {Proceedings of the National Academy of Sciences},
volume = {120},
number = {33},
pages = {e2203828120},
year = {2023},
doi = {10.1073/pnas.2203828120},
URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2203828120},
eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2203828120},
}

4 changes: 3 additions & 1 deletion inst/pages/differential_abundance.qmd
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Expand Up @@ -503,12 +503,14 @@ design or data type. Commonly used DAA tools include:
- ALDEx2 [@Gloor2016]
- ANCOM [@Mandal2015]
- ANCOMBC [@ancombc2020]
- BIRDMAn [@Rahman2023]
- corncob [@Martin2021]
- DACOMP [@Brill2019]
- DESeq2 [@Love2014]
- eBay [@Liu2020]
- edgeR [@Chen2016]
- fastANCOM [@fastANCOM2022]
- fido [@Silverman2019]
- LDM [@Hu2020]
- lefser [@Khlebrodova2021]
- limma [@Ritchie2015]
Expand All @@ -517,9 +519,9 @@ design or data type. Commonly used DAA tools include:
- metagenomeSeq [@Paulson2017]
- Omnibus [@Omnibus2018]
- RAIDA [@Sohn2015]
- sccomp [@mangiola2023]
- t-test
- Wilcoxon test
- ZicoSeq [@Yang2022]
- ZINQ [@Ling2021]
- BIRDMAn [@Rahman2023]
:::

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