Jona

Currently, netSmooth uses PCA or tSNE for dimensionality reduction, clustering, and robustness. We should also implement UMAP for this. - find the most suitable umap library for R - add...

to make netSmooth work with large, disk-based matrices (the `DelayedArray`, `HDF5Array` class, probably). - make sure netSmooth uses the same amount of memory regardless of the size of the _data_...

Fails to install with pipenv

1

Perhaps it's time to extend support to python > 3.6?

``` lib/python3.6/site-packages/sklearn/base.py:420: FutureWarning: The default value of multioutput (not exposed in score method) will change from 'variance_weighted' to 'uniform_average' in 0.23 to keep consistent with 'metrics.r2_score'. To specify the default...

scipy 1.3 introduced a rewrite of `stats.pearsonr` [1] which broke the `test_utils.test_correlate_factors_and_features` test. This needs to be investigated - should only the test be rewritten, or the whole "feature correlations"...