Tamás Stirling

Disregard axis labels when positioning legend boxes

4

Hi, Maybe not an issue, but I couldn't get this to work: FigA has very long y axis labels at the right side of the plot. FigB has a legend...

Related to #462, #716, #737. In my data set the dates are sometimes truncated: ``` df

Using web history instead of ids returns more results than expected

5

When I run `entrez_search()` with `use_history` and `retmax = 5`, the function will respect this and return 5 UIDs: ``` biosample_uid

mulea

17

Dear Bioconductor Team, With this issue we would like to submit the `mulea` package. `mulea` is a comprehensive overrepresentation and functional enrichment analyser R package which reads ontologies (gene and...

Pastml should stop with an error when internal node labels are not unique

1

It took me a while to discover that the reason I was getting funky pastml results was that my input tree had redundant internal node labels. While this is clearly...

Classification with reads instead of assembled genomes?

3

In my data set unfortunately many genomes have low ("None" or "Low") confidence for the CPS type for Klebsiella. I understand this may be due to sequencing error or failure...

I've recently started using your package, many thanks for developing it! After fitting the tree with `dater()`, when I call `outlierTips()` on the fitted tree, a data.frame is printed to...

Use some fixed colors generate the rest

1

Hi, many thanks for developing this package! I have an application where I have some fixed colors and want to find optimal colors for the rest of the character levels...

Related to issues #63, #69, #76. `db_download_gbif()` downloads an SQLite version of GBIF from Amazon S3. This SQLite version is automatically updated every day using this pipeline: https://github.com/sckott/gbif-backbone-sql. However, every...

Query works with taxize but doesn't work with taxizedb

5

Hi, This function from the **taxize** package works: ``` r taxize::classification("podoviridae", "ncbi") #> No ENTREZ API key provided #> Get one via taxize::use_entrez() #> See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ #> ══ 1 queries...