From 7f9fc407701aac953fadd4ffa823eb77190accb7 Mon Sep 17 00:00:00 2001 From: Daena Rys Date: Tue, 6 Aug 2024 13:56:05 +0300 Subject: [PATCH 1/2] v1: docs- cite MGnifyR with notebook references Signed-off-by: Daena Rys --- inst/pages/miaverse.qmd | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/inst/pages/miaverse.qmd b/inst/pages/miaverse.qmd index 343d94e6..c503b7f4 100644 --- a/inst/pages/miaverse.qmd +++ b/inst/pages/miaverse.qmd @@ -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](http://github.com/beadyallen/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/) From b84b138221a7f6836012bf08bc45fe3d3ec5d161 Mon Sep 17 00:00:00 2001 From: Daena Rys Date: Tue, 6 Aug 2024 14:16:52 +0300 Subject: [PATCH 2/2] v2: docs- update link Signed-off-by: Daena Rys --- inst/pages/miaverse.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/pages/miaverse.qmd b/inst/pages/miaverse.qmd index c503b7f4..49ca6129 100644 --- a/inst/pages/miaverse.qmd +++ b/inst/pages/miaverse.qmd @@ -121,7 +121,7 @@ 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 -- [MGnifyR](http://github.com/beadyallen/mgnifyr) for accessing and processing MGnify data in R +- [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