matthew
matthew
`geom_tiplab` is causing conversion to `plotly` via the `ggplotly` function to fail, and produces a nonsense chart. Here is a minimal reproducible example [from the tree data book, section B.1](https://yulab-smu.top/treedata-book/related-tools.html):...
I noticed other *Issues* that mention that Biopython-1.79 is causing warnings and crashes. I thought I would report that I see the same warnings, but the `iss generate` command still...
The result of `salmon quant` (quasi-mapping + SA) for the same paired-end read input differs when run with `--libType A` versus `--libType ISF`, even though Salmon correctly infers that the...
I am developing a package which implements extensions to `parsnip`. I am trying to understand the `parsnip` design principle of a *model* versus an *engine* so that I can implement...
I am constructing a `parsnip`-adjacent package that implements a new `parsnip` model with several engines. The algorithms underlying each engine for the common new model are quite heterogeneous, to the...
For many circular genomes, gene annotations in NCBI RefSeq overlap the "end" of the linear representation, i.e. the arbitrary nucleotide chosen to be "position 0" for the linear representation of...
When the `-nameOnly` flag is provided to `getfasta` and strandedness is also enforced with `-s` , then it still appends the strand information to the output sequence name, e.g. `>my_sequence(-)`...
analogous issue to #406, but for the TCN architecture.
I am observing high relative error when comparing two approaches for computing the signature of a path. I am writing to confirm if the high relative error is expected, or...
Unable to install `pysurvival`. Here is the version information: OS: MacOs Monterey 12.3.1. ``` % python3 --version Python 3.10.7 % pip3 --version pip 22.3 from /Users//lib/python3.10/site-packages/pip (python 3.10) % gcc...