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Installed using the docker installation methods (docker pull, docker run, etc).
Pulled from a find_trees.py result for: Neisseria
time physcraper_run.py --study_id pg_2757 --tree_id tree6369 --t…
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Presently, exported functions of the package API use `pk_` as the prefix, which is short but has several shortcomings. For example, it is not a prefix we use anywhere else in Phenoscape, yet it is fre…
hlapp updated
3 years ago
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Improve parameter handling in [get_ontotrace_data()](https://github.com/phenoscape/rphenoscape/blob/ff42f3f355fc87c9293aecacbf520f1b5bd6b073/R/pk_ontotrace.R#L120-L174).
This issue was broken out o…
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Some of the function documentation examples are wrapped in `dontrun` blocks even though the code runs fine.
Consider removing these `dontrun` blocks so the HTML documentation will be more informative…
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@sckott I think JQ could be a pretty good way to define mappings between, say, description of a Dataset using schema.org and a description in a JSON-ified version of EML or NeXML. I dunno, maybe woul…
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The `RNeXML documentation` link in the rphenoscape vignette is no longer valid and results in a 404 webpage. Update the RNeXML link to the new location for this documentation. The correct link is http…
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Replace for loops with an appropriate apply function that is more expressive.
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```
> absence_mat_median_fins sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
```
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Hi! I am using a Mac (BigSur) for running VMD. I ran 1us simulation in Desmond on a Linux box (copied output on Mac) and wanted to run PCA analysis. In VMD when I load the molecule (and the trajectori…
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Add gene name from treebase? Matrices labelled in nexml?