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Hi,
I am quite new to microbiome analysis and, frankly, quite at a loss as to how to proceed. So, I apologize is my question is naive or has already been answered elsewhere. I have just read a paper …
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- improving examples for methods
- solving documentation warnings (when packages are loading or installing)
- Improving methods' argument description
- improving the transparency of the method used in…
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I applied your script on my data. As you can see in the metadata I have a column called traitment with ( CTRL , TR1 ,TR2 and TR4)
ko_abundance_file
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Hi!
I tried PIME package using this pipeline:
```
pime.oob.error(phyloseq, "phenotype")
phy_BrDi
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### Welcome Outreachy Applicants!
Note: This task can be completed by multiple Outreachy applicants.
### BugSigDB Project
BugSigDB is a wiki built to capture standardized microbial signatures of …
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We noticed recently that doing quantification multiple times (using exact same settings) on the same file using salmon v0.99.0 resulted in some transcripts having different read number values (NumRead…
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Hi,
My relative abundance table reads like this:
genus | control-1 | control-2 | case-1 | case-2 |
--- | --- | --- | --- | --- |
Colwellia | 0.51 | 0.35 | 43.3 | 56.4 |
Pseudoalteromonas …
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Hello,
I have a quick question about tax4fun2. Is it possible to generate a file that has the KO annotations for each individual ASV/OTU in my dataset? Ideally I would like to be able to do thing…
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Hi, @mcalgaro93, when using the createPositives function, does using `slot = "pValMat", colName = "rawP", type = "pvalue"` (positives1 object in the code below) mean that the features are ranked by ra…
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Hello,
I was able to get LOCOM working on my 16S SSU count table and have created a "res" object based on one of my binary metadata variables:
`res