John Lees

Fitting null with perfect separation

1

This dataset fails: http://klif.vet.uu.nl/pyseer/genomes/

Add recipe for sdsl-lite v3

16

See discussion at https://github.com/xxsds/sdsl-lite/issues/91#issuecomment-965617905 This repo is a fork of sdsl-lite (already on conda-forge). The upstream repo is no longer maintained, and this is a major version update. Checklist -...

Also pin joblib version to fix CI for now Closes #231

See: - https://github.com/scikit-learn-contrib/hdbscan/issues/562 - https://github.com/scikit-learn-contrib/hdbscan/issues/565 - https://github.com/scikit-learn-contrib/hdbscan/issues/569 New release of HDBSCAN will fix this, but if delayed should pin joblib

If scientific notation is used in the dot file, e.g. `1e-5`, this cannot be read by microreact. We need to either rescale the output, remove the scientific notation, or put...

> Another thing I noticed when doing the cytoscape network visualisation is that my query samples are not included in the .graphml component files. They are included in the one...

I would find it really handy if we could load vcfs into this viewer. I think a modified version of the code to show manhattan plots might do the trick....

See https://eigen.tuxfamily.org/dox/classEigen_1_1LLT.html https://eigen.tuxfamily.org/dox/classEigen_1_1LDLT.html https://eigen.tuxfamily.org/dox/TopicUsingBlasLapack.html

See https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac564/6674501 Shoukd be faster

HDF5 file needs to be split into multiple groups

1

When there gets to be >500k or so sketches in the sketch group performance gets very slow, looks like it's because the metadata cache size isn't large enough: https://forum.hdfgroup.org/t/limit-on-the-number-of-datasets-in-one-group/5892 I...