Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add DAA methods #647

Merged
merged 1 commit into from
Dec 2, 2024
Merged

Add DAA methods #647

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 14 additions & 0 deletions inst/assets/bibliography.bib
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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]
:::
Loading