gggenomes
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thackl
A grammar of graphics for comparative genomics
`read_gff3()` is based on `readr::read_tsv()`. I use its `comment="#"` to skip comment lines. However, `read_tsv()` treats every occurrence of a "#" as the start of a comment, not just at...
`read_seqs(".fna/.gbk/.gff")` and `read_gbk()` use non-R parsers to preprocess the data before reading them into R. This is just done by turning the file argument provided to the `read_*` function ("foo.fna")...
Right now, filtering can easily be done at runtime using `...` in `pull_*` functions. But it might make sense to provide this also as an external function. In particular in...
There still a lot of stuff in flux. Would be very useful to have some sort of idea which functions are stable/maturing/experimental, ... https://lifecycle.r-lib.org/articles/lifecycle.html include with `r lifecycle::badge("deprecated")`, see https://github.com/tidyverse/tidyr/blob/master/R/nest.R
Make sure all geom's have proper documentation and examples
Add functionality to visualize methylation patterns or ChIPseq results. This needs good example data first.
Use tracks to show expression over different conditions/timepoints. Show, for example, viral infection cycle - link to genomic organization
Add functionality to visualize GWAS-style data etc. Would need to find good example data first, though.