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```r
> re_deblur %>% MicrobiotaProcess::filter(Sample=="g_Rahnella")
Error in validObject(.Object) :
invalid class “SummarizedExperiment” object:
nb of cols in 'assay' (1) must equal nb of…
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Hi!
It is possible to extract from raw data forward and reverse reads assigned to specific ASVs?
for example: I need to extract raw reads pairs which were identified as "Cyanobacteria" and get fil…
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Hello,
I am trying to extract upper taxonomic level information for the taxa I have in genus level. For 'itis', the function upstream() works, but for some levels it produces incorrect results. Whe…
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Hi Daniel
I'm having some issues with building alternative universal models using CARVEME (such as with the alternative biomass reactions). If i run
``` build_universe --curated```
I get th…
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**Describe the bug**
There are a couple orders of magnitude too many rows that cannot be matched to the phylogenetic tree. We need to get to the bottom of why hundreds of rows are unmatched.
**To …
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Hi,
I was wondering if it would be possible to add support for reports produced by Kaiju.
Pavian is an amazing piece of visualisation software, thank you very much for coding it.
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Hello!
I am trying to use this tool & running into a weird error - here's the log file
Loading packages...
Intermediate results will be stored in /fs/project/PAS1331/cyanobacteria/VirHostMatch/V…
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Hi,
I am looking forward to using **lca summarize** to see the different taxonomical compositions of my metagenome.
From my first test runs and your documentation [1] it looks like I'm only seeing t…
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This one should probably not be in Bacteria when the verbatim data says `Animalia > Chordata`
```
{
"count": 1417,
"verbatim_kingdom": "Animalia",
"verbatim_phylum": "Chordata",
"verba…
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hello,
Can I model abundance distributions of functional genes and to simulate corresponding shotgun metagenome datasets?
Very thanks!
chunxu