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In microbiome time series analyses we have the definitions of abundant taxa, conditionally rare taxa, persistently rare taxa and other rare taxa (see e.g. the two refs below).
Conditionally rare …
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The pipeline ran after removing the samples which was resulting in error
executor > local (6046)
[a2/6ffd4c] process > QC (69) [100%] 73 of 73 ✔
[c6/b1e07e] process >…
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Hello,
Kind of a weird 'issue' as it's more a 'forum like' topic.
I am completely new to JSDMs and have some questions about some thoughts I had about how to use them.
For instance :
- How i…
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Hello
Is there a way to run METABOLIC-C.2nd_run.pl on mock communities? I have whole genomes of nine microbes and I would like to see what the community metabolic profile is at different relative abu…
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**Is your feature request related to a problem? Please describe.**
Absolutely. Compositional data analysis [CoDA] is large in fields such as bioinformatics, geology, and economics.
> In statist…
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Hi there,
I'm wondering about the assignment of BVAB(1/2/3) as you say that VALENCIA only considers species level annotation for Lactobacillus, Gardnerella, Prevotella, Atopobium and Sneathia, but…
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We could use the approach from Steffensen et al. 2017 (linear relationship between CPUE and RD abundance estimates) to provide presumably more accurate initial abundances by segment and origin given t…
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Hi,
I'm trying to use fantaxtic to get the top 10 most abundant genera across a complete phyloseq object and list the relative abundances of these top genera. I was trying to do this like so:
`…
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Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome - Zhen _et al_ - BMC
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-0222…
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Hi guys
Thank you so much for plot_tree() it is making things easier.
Could you please help me with my queries;
1- According to the info you provided about the function that the points represente…