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Hi Developer,
Thank you for developing this tool. Applying it to feature count data is quite straightforward. As you know functional information is also important for the microbiome data. I was wonde…
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When I run
`knit("PartIIphyloseq.rnw")`
I get:
`Warning messages:
1: In is.na(e1) | is.na(e2) :
longer object length is not a multiple of shorter object length
2: In`!=.default`(Phylum, c("", "un…
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in the function name_bad_taxa:
change “row_name" to “asv” for lines 227, 251, and 252
add dpylr:: to line 248: “dplyr::select(asv, rank, bad_label) %>%"
when using the function:
curated_ps_obj
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### Description of the bug
When running the workflow with "--dada_ref_taxonomy silva=132" option it fails at the SUMMARY_REPORT generation stage. The error I get is as below.
Upon a closer look at t…
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Hello.
As described in previous issues #10 and #47 the problem remains:
tens and tens of lines full of:
```
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
…
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Hi!
After finishing the workflow with shiny-phyloseq I tried to use Provenance-panel to save the code. Both buttons on the page (“Download Archive” and “Preview code”) give the same error: “object '…
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Hi,
There's an issue going on with Phyloseq's installation via devtools::install_github (from https://joey711.github.io/phyloseq/install.html)
`library("devtools")`
`install_github("phyloseq/joey…
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Here is the error
```
> ps_obj #Data quality control
> library(metacoder)
> obj$data$otu_counts
> print(obj)
1186 taxa: aab. Bacteria, aac. Bacteroidota ... cjf. uncultured_delta, cjl. un…
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Hello everybody. I am using the following script:
### Difference of our samples at specific taxonomic levels ###
# In order to grow up all the OTUs that have the same taxonomy at a certain taxon…