Adam Boxall issues

Results 9 issues of


                                            Adam Boxall

clustering requires manual downstream processing, but is resource intensive

no way to export mu and std for active gps from the model conveniently

reference-query training cannot be performed with mismatched gene coverage

An imputation approach is needed for genes which are present in the reference but not in the query.

add simple model evaluation

There isn't a simple catch-all set of figures we can automatically generate to evaluate a new reference model. This could be added to the CLI.

deployment on HPC environments is difficult due to compatibility issues

Proposed solution would be to provide a Dockerfile and instructions for building a docker or singularity image.

add CLI to wrap 'reproducibility' scripts

add minimal tests

There is currently no testing in NicheCompass, but a small number of tests on a minimal dataset (small enough to run in a low-resource setting with a single core) would...

Accumulation of memory usage with large number of dense array queries

Hi, I'm hoping someone will be able to help us resolve a memory issue with TileDB-Py... When running a large number of queries against a TileDB dense array, we are...

Control size of AwsEventLoop thread pool

Hi, I wonder if anyone can help with a configuration question around the AwsEventLoop thread pool associated with a TileDB context. It seems the size of this thread pool defaults...