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I often have count tables that have an empty string in the header that marks the OTU/ASV column. So far I could not find a way to handle this directly and replaced by "ASV" (using `sed`). It would be …
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I'm running into trouble calculating unifrac distances in phyloseq. I keep getting the following message whenever I run the distance function with weighted or unweighted unifrac:
`Warning message: …
cwatt updated
6 months ago
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Hi
This problem is very similar to [Issue 961](https://github.com/benjjneb/dada2/issues/691).
The sequencing is from a big Novaseq run of the protein coding gene rpoB so I do have 400,000 unique…
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Hi there,
I've been running code off of the vignette simply substituting in my own phyloseq object.
I have a treatment * day model for the effect of a supplement over time:
phyloseq-class exp…
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Hello! I'm trying to test RadEmu on a fungal ITS phyloseq object and am receiving this error:
_Error in intI(i, n = di[margin], dn = dn[[margin]], give.dn = FALSE) :
index larger than maximal …
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Hello,
I am trying out fantaxtic. I am having some issues though in that it apparently is seeing some of the sample names as being duplicate.
The code I am using is as follows and the code itself wo…
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Hi, there!
These days I'm trying to visualize the α diversity of different microbiome data, the problem is **whatever the data is, the Chao1 index and observed index were always the same, and thus th…
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```bash
singlem summarise --input-archive-otu-table-list ...
```
triggers an error:
```
Exception: Summary requires input OTU tables, archive OTU tables, or taxonomic profiles
```
I think…
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Hi,
I am using vegan::fisher.alpha(). My test data is
```
> otu_table(GAGA_ampSeq.physeq.rarefy)[1:10,20:24]
OTU Table: [10 taxa and 5 samples]
taxa are rows
…
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Hi,
I'm trying to plot ordination plot, so I used the below code:
```
ps0 %>%
tax_fix() %>%
phyloseq_validate() %>%
tax_transform("clr", rank = "Genus") %>%
dist_calc(dist = "wunifr…