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Since I am have been facing difficulties in shiny with dynamically creating inputs for the config (see: #1), I will try to implement other parts of the shiny app using an pre-initialised config.
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While my criticism of the calibration in #89 was hasty, I think one of its points remains.
We currently do not allow calibration of a tip, but I think that's a very frequent use case for calibrations…
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@matsen and I have been talking through an idea about how we might organize data around cft and cftweb (and perhaps other projects) to facilitate interoperability.
## Problem statement
Take a cs…
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HI @rneher and team phyloTree,
I am interested in making a pared down version of augur+phylo tree that lets you quickly generate interactive trees. I have in mind something similar-to but far simpl…
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Hi,
is a newick parser on the road map, or do you intend to rely on the R interface for now?
Thanks!
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I was wondering if it is possible to get the Greengenes reference sequence ID used to assign taxonomy to the sequence variants inferred by dada2. This information is useful for other pipelines such …
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Basic tree statistics functions (for example, `tree.width`) require loading config file. This is not the case when running the test suite, since the config file is loaded prior to testing said functio…
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After loading the species tree from newick format and creating the tree structure set the following the τ and θ parameters.
## τ
For each inner node of the species tree we set one …
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- Repository: https://github.com/klarakaleb/roma
- [x] I understand that by submitting my package to _Bioconductor_,
the package source and all review commentary are visible to the
general pu…
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Hello,
Is it possible to save the tree produced by plot_tree (Phyloseq) to a newick format with only OTU or/and Taxonomic names?