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```R
> set.seed(1234)
> outer phy plot(phy)
Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
> phy…
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```R
get.integration.times
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These simulations will be used to determine the integration time of sequences recovered from latent viral reservoir.
- [x] Using twt simulate within-host dynamics that:
> Sample sequences from th…
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Related to https://github.com/PoonLab/bayroot/issues/14
It should be possible to export a "transmission tree" as a Newick tree string that is annotated with both transmission (branching) and transf…
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by Kentaro Itokawa (National Institute of Infectious Diseases, Japan) (_Edited_ 2021-12-29)
This potential sublineage includes >280 _(Edited)_ genomes so far in GISAID (searched for AY.29+S:Q414R i…
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hey @jodyphelan when I ran these SRA Accession Number on TB-Profiler_v4.0.1, v4.0.1, v4.0.2, v4.0.3 in conda Package and Docker Container it is showing that it is sensitive for all drugs, while these …
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A sublineage of AY.4 with Orf1a:T4083M seems to grow in some european countries
First sequences : UK 33w/2021
Last sequences Switzerland 45w/2021
Total sequences: 1937 sequences (Europe: 1907)
E…
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Hi John,
found this project today, got it running and I'm amazed. :)
Guess I will switch from my own build quite basic python dash app to your shiny app. However I would like to know about adding …
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**Is your feature request related to a problem? Please describe.**
Hello, I am trying to use TB profiler for predicting the drug resistance of a batch of 65 Mtb genomes. Unfortunately we only have wi…
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Lineage transmitted from Latentcomp_86 to US_Active_type_387 (Latent to Active), however in the event log the ```type``` of both compartments are "Active".
event_index | event.type | Time | linea…