orthogene

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## 1. Bug description When running conver_orthologs I get an error that I am trying to set attribute to NULL. ### Console output ``` Preparing gene_df. data.frame format detected. Extracting...

shanie-landen

orthogene fails rcmdcheck when ape isn't installed

1

`ape` is only in Suggests, but it is called here: https://github.com/neurogenomics/orthogene/blob/bc242c50396018d55fd12e653c0c069bc34dca67/R/prepare_tree.R#L129-L130 This is ultimately called in one of the examples for `plot_orthogene()`: https://github.com/neurogenomics/orthogene/blob/bc242c50396018d55fd12e653c0c069bc34dca67/R/plot_orthotree.R#L54 If ape is not installed rcmdcheck then...

willgearty

- [f1000](https://f1000research.com/about) - [Bioinformatics](https://academic.oup.com/bioinformatics) - [eLife](https://elifesciences.org/)

bschilder

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901538/ https://github.com/ropensci/taxize > taxize allows users to search over many taxonomic data sources for species names (scientific and common) and download up and downstream taxonomic hierarchical information - among other...

bschilder

https://zoonomiaproject.org/the-data/ >TOGA annotation of orthologous genes >Annotation of genes across the 240 Zoonomia species —plus many more — inferred using [TOGA](https://github.com/hillerlab/TOGA) (Tool to infer Orthologs from Genome Alignments). Files are...

bschilder

Replace `ggtree`/`ggimage`

1

`ggtree`/`ggimage` seem to be struggling to keep up with maintenance in a timely manner, and are causing `orthogene` to break. https://github.com/YuLab-SMU/ggtree/issues https://github.com/GuangchuangYu/ggimage/pull/45 https://github.com/GuangchuangYu/ggimage/pull/46 Consider switching all functionality to `rphylopic`, if...

bschilder

**Describe the solution you'd like** Provide output of `convert_orthologs`in gene formats besides gene symbols (e.g. ensembl IDs). **Additional context** Relevant Issue: #15

bschilder

Identifier mapping to Ensembl identifiers

4

I tried to figure out how I can change the output to Ensembl identifiers instead of gene symbols. I tried adding the argument "numeric_ns="ENSG" but that didn't help. Do you...

mkutmon

Functions like `map_genes` and `aggregate_genes` rely on "gprofiler" as the only method that can do gene synonym matching. However, this requires internet access and the gprofiler databases sometime breaks down...

bschilder

`plot_orthotree` will seem to randomly drop some species (that are indeed available) when `mc.cores>1`, which parallelises certain steps with `parallel::mclapply`. I'm not sure why this happens, but it does perhaps...

bschilder