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Hi there
Maybe a basic question but I'd like to ask what people's opinion is of using DESeq2 within SQMtools for differential abundance of taxa? It's obviously possibly with SQMtools to compare dif…
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Let's tackle differential abundance as it will be one of the priorities for this work. I suggest starting to look at the R code starting from this line of one of my past projects, where the `fitZIG` f…
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Hi there,
First of all, thank you for this really helpful package!
I converted the KO IDs to the KEGG IDs using the "ko2kegg_abundance" function because I'm more interested on KEGG IDs.
For thi…
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In this manuscript DAA methods have been benchmarked and a new method was proposed: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01320-0 we should check if any of these meth…
mlist updated
2 months ago
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I am doing some differential analysis of 16s rRNA data and following code in this vignette:
https://joey711.github.io/phyloseq-extensions/DESeq2.htm
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sigtab
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Results panel for differential abundance tests. Maybe even include corresponding QA plots, etc. If done well, this could be really nice. And a good demo of your score-versus-taxonomy ggplot that has b…
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Dear m6A developers.
I wonder if you can advise on the best statistics to perform a differential m6A abundance analysis between two sample groups.
I've already successfully run m6anet v2.1 on my O…
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Hello,
Thank you very much for developing MIcrobiomeAnalyst, I have enjoyed using it. Unfortunatly since yesterday differential abundance analysis is down on its webserver and I cannot install the R…
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After talking to @qiyunzhu , it is becoming clear that skbio would need to have a differential abundance method that can at least provide directionality (i.e. features increase / decrease in abundance…
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Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer - Xujun Liang - Scientific Reports
https://www.nature.com/articles/srep04985