MaAslin2-Tutorial #5173

renu-pal · 2024-07-16T21:40:59Z

Tutorial draft on Maaslin2. Would love any suggestions or changes on this.

shiltemann · 2024-07-30T09:58:59Z

Hi @renu-pal, thanks for your contribution! I have taken it out of draft mode so that our tests can run and people will know they can review it :)

topics/microbiome/tutorials/multivariable-association/tutorial.md

Co-authored-by: Saskia Hiltemann <[email protected]>

renu-pal · 2024-07-30T10:06:42Z

Hi @renu-pal, thanks for your contribution! I have taken it out of draft mode so that our tests can run and people will know they can review it :)

Sounds great! :)

paulzierep

Looks great! would be nice to extand a bit, show different options and some more output

topics/microbiome/tutorials/multivariable-association/data-library.yaml

topics/microbiome/tutorials/multivariable-association/tutorial.md

paulzierep · 2024-08-15T09:57:48Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+>
+{: .agenda}
+
+# Get the data


Where does the data come from, what does it contain, was it used in other studies, are there other studies that suggest ideal maaslin2 parameters for this kind of data ?

I couldn't find studies which used both HMP2 data as well as Maaslin2 tool. So instead I mentioned studies which used Maaslin2 tool with the parameters used. If it does not feel right , then please let me know.

Isn't the main maaslin2 paper using HMP data ? https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009442#sec002

Maybe its enought to add that this was the initial data used to demonstrate maaslin2 ?

topics/microbiome/tutorials/multivariable-association/tutorial.md

paulzierep · 2024-08-15T10:19:19Z

Can you look into the linting issues as well ?

bgruening · 2024-09-07T12:22:49Z

@renu-pal do you need any help here?

renu-pal · 2024-09-08T23:07:08Z

@renu-pal do you need any help here?

Definitely @bgruening :) . Can you please go through the tutorial and let me know if you find anything wrong.

topics/microbiome/tutorials/multivariable-association/data-library.yaml

...-'Determining-multivariable-association-between-various-meta’omic-features-using-MaAslin2.ga

topics/microbiome/tutorials/multivariable-association/tutorial.md

…rary.yaml Co-authored-by: Björn Grüning <[email protected]>

paulzierep · 2024-09-30T13:39:03Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+>
+{: .agenda}
+
+# Get the data


Isn't the main maaslin2 paper using HMP data ? https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009442#sec002

topics/microbiome/tutorials/multivariable-association/tutorial.md

paulzierep · 2024-09-30T13:47:24Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+- **Sensitivity** measures how well the methods detect true signals, higher values lead to better performance.
+- **False discovery rate (FDR)** measures the proportion of false positives among detected signals (lower FDR is better).
+- MaAsLin2 is the clear standout for both differential abundance detection and multivariable association detection, showing high sensitivity and maintaining a low FDR.
+


Maybe we can add something like:
In this regard, MaAsLin2 can be seen as a Swiss army knife for differential analysis of microbiome data. With some text processing various omics data types could be used as input e.g. from these GTN tutorials:

then check the existing GTN toturial and add those that provide matching data

bla

blumb

paulzierep · 2024-10-01T08:30:56Z

topics/microbiome/tutorials/multivariable-association/data-library.yaml

+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: The new topic


Suggested change

- name: The new topic

- name: The new topic

?

topics/microbiome/tutorials/multivariable-association/tutorial.md

paulzierep · 2024-10-01T08:40:50Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+| **Phyloseq + DESeq2**| Strong for RNA-seq and transcriptomics; integrates with Phyloseq | Lacks compositionality awareness         | While DESeq2 works for microbiome data, MaAsLin2 offers more suitable options for compositional data and covariate handling. |
+| **Limma-Voom**      | Effective for RNA-seq and microarray data, handles low counts | Not tailored for compositional microbiome data | Limma-Voom is well-suited for gene expression, but MaAsLin2 better accounts for the unique characteristics of microbiome data. |
+
+- ANCOM-BC and MaAsLin2, outperform general-purpose tools like DESeq2 and limma-voom when it comes to microbiome data. This is due to their handling of the compositional nature of microbiome data and the sparsity typical of microbial datasets.[PMID: 36617187](https://pubmed.ncbi.nlm.nih.gov/36617187/)


Can you please exchange all links to studies with citations as shown here:

training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md

Line 89 in 5012353

The currently available studies used Illumina sequencing, generating short reads. Longer read lengths, generated by third-generation sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), make it **easier and more practical to identify strains with fewer reads**. MinION (from Oxford Nanopore) is a portable, real-time device for ONT sequencing. Several proof-of-principle studies have shown the **utility of ONT long-read sequencing from metagenomic samples for pathogen identification** ({% cite CIUFFREDA20211497 %}).

paulzierep · 2024-10-01T08:42:27Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+- **Taxonomy (or features) file**: \
+        This file is tab-delimited.\
+        Formatted with features as columns and samples as rows.\
+        The transposition of this format is also okay.\


Is it ? Can our wrapper work with both ?

paulzierep · 2024-10-01T08:44:15Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+
+MaAsLin2 requires the following input files:
+
+- **Taxonomy (or features) file**: \


Suggested change

- **Taxonomy (or features) file**: \

- **Features file**: \

Would like to keep it more generic. Maybe add some examples like: (OTU/ASV abundance table, MAGs abundance matrix, taxonomy table, gene count matrix at the end of the list

paulzierep · 2024-10-01T08:45:14Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+>
+{: .agenda}
+
+# Get the data


Maybe its enought to add that this was the initial data used to demonstrate maaslin2 ?

paulzierep · 2024-10-01T08:45:28Z

topics/microbiome/tutorials/multivariable-association/tutorial.md

+        Formatted with features as columns and samples as rows.\
+        The transposition of this format is also okay.
+
+The Taxonomy file can contain samples not included in the metadata file (or vice versa). For both cases, those samples not included in both files will be removed from the analysis.


Suggested change

The Taxonomy file can contain samples not included in the metadata file (or vice versa). For both cases, those samples not included in both files will be removed from the analysis.

The feature file can contain samples not included in the metadata file (or vice versa). For both cases, those samples not included in both files will be removed from the analysis.

Co-authored-by: paulzierep <[email protected]>

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Co-authored-by: Saskia Hiltemann <[email protected]>

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MaAslin2-Tutorial #5173

MaAslin2-Tutorial #5173

renu-pal commented Jul 16, 2024 •

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		MaAsLin2 requires the following input files:

		- Taxonomy (or features) file: \

	The Taxonomy file can contain samples not included in the metadata file (or vice versa). For both cases, those samples not included in both files will be removed from the analysis.
	The feature file can contain samples not included in the metadata file (or vice versa). For both cases, those samples not included in both files will be removed from the analysis.

MaAslin2-Tutorial #5173

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MaAslin2-Tutorial #5173

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renu-pal commented Jul 16, 2024 •

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