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Hi,
I am trying to apply tax_glom function on my phyloseq object. But looks like it is not working.
The dimensions of the file I am working on is 768 OTU and 201 samples
The code I used:
OT…
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(copied from https://github.com/sourmash-bio/sourmash/issues/461#issuecomment-1993390314)
Hi Titus @ctb , I don't know whether I could ask the following questions related to this issue, anyway....
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Hi,
I don't know if this question is redundant but my first search on this topic was unsuccessfull and I'm still a beginner in this field.
I have microbiome data from two marker genes 16S and a fun…
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Hello,
I was hoping you might have some advice about understanding an issue I am running into with some microbiome samples (fungal community in soybean at ITS region).
The issue has to do with i…
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We noticed that the latest PR2 release contains only one file for DADA2 annotation, compatible with assignTaxonomy based on a naive Bayesian classifier. However, we wanted to get species-level identif…
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Cf https://doi.org/10.3389/fmars.2021.620702
And in particular:
INDETERMINABILIS (INDET.) The ON sign _indet_. is taken to mean that
the taxon is indeterminable beyond a certain taxonomic level…
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We are getting closer to being able to separate out the lineage stuff from the revindex stuff in LCA, so we could envision combining searches on signatures and SBTs with taxonomic reporting (where ava…
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Hi @wegnerce ,
Im currently working on metatranscriptome of plant samples as well and i've been referring to this amazing work for as a guidance for my bioinformatic analysis. Im very new to all bi…
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**context**: occurrence search; some IUCN Global Red List Category assignments to occurrence records are incorrect
**example issue**: _Betula pubescens_ should be "Least Concern (LC)", but shows as…
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Dear @torognes, are you planning to add the sintax classifier http://biorxiv.org/content/early/2016/09/09/074161?
Thank you,
Davide