-
Hi,
I am currently running your pipeline and yould like to suggest a few problems I stumbled upon while following the readme.
Under *2. Downloading RESCUE Files*:
tar –xvzf ./databases.tar.gz --…
-
Dear all,
I was following the phyloseq tutorial to create a heatmap. But with three soil and 12 plant genotypes as factor the figure was not too explanatory. Can someone here help to create a heat ma…
-
`DESeq2` is a package design to use it for RNAseq data, but also you can use this library with metabarcoding data. I want to use `DESeq2` package to find OTUs that differ in categorical variables. The…
-
I am suddenly getting an error with "phyloseq_to_deseq2" command even with the scripts which used to run before.
```
> diagdds24 = phyloseq_to_deseq2(pvl24, ~Treatment)
converting counts to intege…
-
otu_mat %>% tibble::column_to_rownames("otu")
tax_mat % tibble::column_to_rownames("otu")
samples_df%tibble::column_to_rownames("sample")
otu_mat
-
Hello dear bioinformaticians colleagues,
I have encountered something "weird", I'm using both ade4 and plot_ordination in my routine, and just found out that ord(physeq) and dudi.pco(psmelt(physeq))…
-
Hello,
I'm relatively new to the phyloseq and DADA2 pipeline.
I have an ASV table that contains the taxonomy and the metadata.
I have to transform it to a phyloseq object, to visualize the relative…
-
Hi,
I have transform the count in **relative abundance cpm** in phyloseq object but still in range command it shown awkward number, I want to use these relative abundance cpm for further beta diver…
-
Hi there,
I have a very basic question and I apologize for redundancy if this has been previously addressed, but I couldn't find an issue with quite the same problem. I am trying to filter my phylo…
-
Hi Joey
Would it be possible when creating phyloseq objects to report samples and OTUs lost?
This is more for project management purposes than for PhyloSeq purposes, but occasionally (quite often) p…