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This was brought up in https://github.com/greenelab/tribe/pull/8, but was proving to be too involved for the scope of the pull request.
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When I am using kraken2 (with standard database) my output looks like this:
```
5.65 10 10 U 0 unclassified
94.35 167 0 R 1 root
94.35 167 0 R1 131567 cellular organisms
92.66 164 0 D 2 …
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In the 2024-01-25 presentation, it was clear that most of the class finished within 70min, for a planned 120min session.
In addition, the initial workshop exercise starts students with a difficult …
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https://bioentity.link//#/publication/10.1093/genetics/iyae189
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Dear Guang:
I am trying to compareCluster for two list of enriched locustag for my bacteria Pseudomonas aeruginosa PAO1. so it does not have a org.db. I can do enrichKEGG using just the locustag and …
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Hi all!
After understanding how pyrazolopyrimidine is bound to **_Pseudomonas aeruginosa MurC_** (#36), we decided to synthesise pyrazolopyrimidines (#35): **AZ5595 (compound 9)** and its correspo…
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Hi, I would like to analyze my shallow shotgun metagenomics data according to the OGU method, https://journals.asm.org/doi/10.1128/msystems.00167-22
The recommended aligner is Shogun, especially I as…
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Activity tables have variable numbers of columns and may have parameters (e.g. concentrations). Ideally we should transform to denormalised (e.g tidytables) but that comes later.
Here we try to a…
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### Bacterial Quorum Sensing and Microbial Community Interactions
_DOI: [10.1128/mBio.02331-17](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964356/pdf/mBio.02331-17.pdf)_
- Introduction:
`…
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Hello, I am running AMRFinderPlus on a large dataset that includes some _Burkholderia mallei_ samples. I specified `--organism Burkholderia_mallei` for these samples, assuming the supported species we…