Mark Farman

Bug in STARFISH annotate code

1

There is a bug in the code that is preventing execution of the bedtools intersect command: [Mon Aug 5 21:10:14 2024] checking formatting of GFFs in ome2gff.txt.. sh: -c: line...

geom_hilight

4

### Prerequisites + [ ] Have you read [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [ ] make sure your are using the latest release version * [ ] read the...

ggbreak has multiple problems

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1. theme(plot.margin) does not work with ggbreak 2. coord_cartesian(clip="off") does not work with ggbreak 3. There appears to be no way to control plot margins to prevent labels from being...

Specifying tree height and width

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It seems there is no way to change tree height to accommodate large numbers of tip labels. I've read suggestions to expand the page size but this will not result...

Unreasonably large introns

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Considering that funannotate was originally developed to annotate fungal genomes, I find it hard to see how it is predicting multiple 7-8 kb introns!

emapper.py has multiple problems

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1. The instructions state that basic usage is as follows: `emapper.py -i FASTA_FILE_PROTEINS -o test` This is not correct if you download the databases to a directory other than the...