-
- `depth2` is being deprecated in https://github.com/microbiomedata/nmdc-schema/blob/issue-486-data-to-7-0 (which will actually result in a new version of the schema, greater than 7.0.0)
- the releas…
-
I thought we would tackle this eventually-- looks like now is good.
We have a few samples of eDNA uploaded (https://geome-db.org/workbench/project-overview?projectId=365). I will be contacting the …
-
A couple of thoughts:
* there will only be an expectation / possibility of encoding factors in high-level functions such as `fetchNASIS`, `fetchSDA`, etc.
* split functionality for further / bet…
-
For @ramonawalls' UA superfund research project we are incorporating some soil datasets from the USGS which are collected from topsoil (xref https://github.com/UA-SRC-data/srpdio/issues/5).
From th…
-
Hi,
I have a problem plotting relative abundance for some of my samples.
This is my phyloseq object, which definitely has an OTU table:
```
> p2
phyloseq-class experiment-level object
otu_ta…
-
Hello,
Kind of a weird 'issue' as it's more a 'forum like' topic.
I am completely new to JSDMs and have some questions about some thoughts I had about how to use them.
For instance :
- How i…
-
Dear developer and other users,
As the title says, I wanna use metaeuk to annotation genome without reference. But I cannot find how to deal with it in manual.
Best
Nana7m1
-
Hi,
I am just started to work with metacoder, but I have a simple question. When I import a phyloseq object with parse phyloseq I can see the all components correctly imported. However, in the otu_t…
-
HI 👋
after importing biom file, it goes with environments as value, not data
I tried to find way to open it as a data frame . the only option I can do to see value as tax_table(data), taxa_n…
-
Posted here!
https://taylorreiter.github.io/2022-07-28-From-raw-metagenome-reads-to-phyloseq-taxonomy-table-using-sourmash-gather-and-sourmash-taxonomy/