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Hi,
It's my first time analysing metagenomics from a shotgun experiment but before to post this issue I tried some strategies to overcome the topic described below.
I would like to construct a phy…
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I would like to use variations of CLR transformation.
e.g., non-zero or iqlr CLR, both using only a subset of the features to estimate the geometric mean.
I can transform a phyloseq object befor…
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Hi,
I have an issue regarding ancombc2 function.
I am working with taxonomic data from metaG and metaT sequencing. I created a phyloseq object and used it as the input data for ancombc2.
However…
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I believe dependencies in phyloseq_inext may be compromised. The function was working for me beautifully maybe a week ago, and now the example code associated with this function is no longer working. …
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Hello,
Thanks so much for providing this great package and so sorry if this is a stupid question. I've been using co_occurrence to get a table of species which co-occur within my microbiome. I'm in…
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Hi,
PIME has been an amazing addition to the microbiome analysis tools I use, thank you for putting it together. I tried using PIME with a phyloseq object that has a tree attached and it doesn't all…
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y aab, NA->aac, aab->aad, aab->aae ... cre->hqm, bjf->hqn, blu->hqo, bwl->hqp
4 data sets:
otu_table:
# A tibble: 42,559 x 43
taxon_id otu_id JZ03601 JZ03602 JZ03603 JZ03701 J…
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this error:
Errore in sort.list(bx[m$xi]) :
'x' dev'essere atomico per 'sort.list', metodo "shell" e "quick"
Si è chiamato 'sort' su una lista?
In aggiunta: Messaggi di avvertimento:
1: : ... …
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This was previously causing an error in the R-CMD-check, which went away when I added the environment flag `_R_CHECK_FORCE_SUGGESTS_` set to false. Ideally we will remove this once the problem with `p…
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### Why this matters
- Users could accidentally set `min_sample_reads` too high and need to know this is why the run fails
- Could occur when doing extreme subsampling, as it is more likely very s…