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Hi Didelot,
I am using the infer_multittree function in the TransPhylo package in R to infer transmission in a group of Mycobacterium tuberculosis clusters from a specific region. However, I am not…
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The LOINC code `48176-2|Deprecated Mycobacterium tuberculosis rifAMPin resistance (rpoB) gene [Presence] in Unspecified specimen by NAA with probe detection` is deprecated: https://loinc.org/48176-2/
…
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```Error executing process > 'vcfpredict:tbprofiler (1)'
Caused by:
Process `vcfpredict:tbprofiler (1)` terminated with an error exit status (1)
Command executed:
bgzip SAMPLE_ID_allelic…
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PTHR10003 Info - IBA to term GO:0005507 for node PTN002224320 with species Mycobacterium tuberculosis negates 'NOT' experimental evidence for term GO:0046872.
PTHR10890 Info - IBA to term GO:0004817 …
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For GO-PathGO alignment
Children of symbiont-mediated suppression of host cytokine production'
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GH Action not updating website :(
Gh-pages peaceiris action is the bit failing:
```
[INFO] ForceOrphan: false
/usr/bin/git clone --depth=1 --single-branch --branch gh-pages ***github.com/Nat…
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I find this pipeline very nice but how can it be used in the analysis of non cancer data?
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I ran `runoak -i simpleobo:hp.obo diff -X simpleobo:hp-latest.obo -o diff.md -O md` and the `Classes added` section looked like this:
Classes added: 932
| Term |
----|
| Mosaic attenuation p…
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* **PTHR ID & PTN node:**
PTN002460893 (PTHR48081)
* **Sequences with problematic annotation (ID + gene/protein name):**
Fly KFase (FBgn0287695/Q9VMC9)
* **Type of Issue: Erroneous source or e…
sjm41 updated
6 months ago
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- GO:0039588 suppression by virus of host antigen processing and presentation >> change label to symbiont-mediated antigen presentation ('processing' not needed in the label)
- 'suppression by vir…