-
A couple of members of my lab and I have been getting very different results when using qiime2 versus phyloseq for calculating weighted unifrac values. It seems that the default parameters used by the…
-
When running normalize_table.py the "taxonomy" observation metadata is not properly encoded in the output file.
1) When using the `-a DESeq2` the taxonomy data is not included at all in the output f…
-
Ref: Pat Schloss' [recent analyses](https://www.biorxiv.org/content/10.1101/2023.06.23.546313v1.full.pdf) on rarefaction in alpha & beta diversity. This addressess well some of the long debates and co…
-
Putting an issue here to collect ideas and track.
I'd advocate still for being able to download, modify, upload, and update metadata to a specific analysis, leaving the original study metadata unto…
-
I tried to rarefay a phyloseq object transformet to a SummarizedExperiment but obtained this Error.
`ps.met.aar = subsampleCounts(makeTreeSEFromPhyloseq(ps.met.aa), min_size = mindeepth, name = "su…
-
Another issue that's come up in this run is that by default, jobs submitted to argo will run only on two of the fourteen GPUs currently available.
To run on the other 12, we usually have to specify:…
-
Hello ONT AmpSeq people.
Im trying to use Ampvis2 inside ONT AmpSeq package, and I use my reads as an input, along with my metadata file that looks like this
SampleID,Group,Condition
bc92,Group…
-
I'm an experient user of Mothur. I use it to teach my students how to analyse 16S sequences.
I noticed 4 bugs in this new version (1.44.1). I am using linux RedHat 7
1 - chimera.vsearch only produ…
-
Several errors are generated, when I execute the examples from the documentation of `plot_rarefaction`, for example:
``` r
library(mobr)
#> Warning: vorhergehender Import 'dplyr::filter' durch 's…
-
Hi,
Would be possible to show SampleIDs in the rarefaction curves plot?
It seems from the available options that this might not be straightforward.
Many thanks,
jose
something like this:
![…