Valentyn Bezshapkin

biplot using FAMD

1

Hello, I think biplots are very informative for PCA. Therefore, I tried to plot "loading scores" of FAMD. Therefore I took column correlations, scaled them by (max - min) on...

I would like to have nomograms from fitted models implemented, as in RMS R package. That would be a really useful upgrade. This form of visual data representation gathers in...

## Description `kneaddata.utilities remove_file` fix for improving intermediate file removal. https://forum.biobakery.org/t/warning-in-kneaddata-utilities-unable-to-remove-file/1538

Hi, thank you for the great software. I think the `tqdm` progressbar would be a great addition for showing ETA with less output in `stdout`. Cheers!

Please, add an ability to process `.csv` and `.biom`, as they are used quite commonly in the field for data representation. Thank you for such an elegant piece of software!

fix: add POSIX functionality for Linux compilation

7

Small fix to compile binaries properly on Linux: - defines `CLOCK_MONOTONIC` in `ggml.c` - Closes #54

[DISCUSSION] Docstrings in codebase

1

For now, a lot of functions and classes remain without documentation. In order to understand their function, purpose and methods it's necessary to dig through a code of a few...

* pharokka version: 1.6.1 * Python version: 3.12.0 ### Description `hmmscan` is slower than `hmmsearch` and might give false positive results, because p-value is corrected for the size of the...

[feature request] query database clustering

1

As `mmseqs2` is already part of the pipeline, it would be nice to see an opportunity to cluster a query database before aligning it against the marker database. Phage genes...

Hello! I've tried using `highquality_clust30` as a reference and identified the following issue. The database has around 200k repeated entries, they appear to be fragmented proteins split on `X` aminoacid....