scvi History#
The scvi-tools package used to be scvi. This page commemorates all the hard work on the scvi package by our numerous contributors.
Contributors#
0.6.7 (2020-8-05)#
0.6.6 (2020-7-08)#
add tqdm to within cluster DE genes @adam
restore tqdm to use simple bar instead of ipywidget @adam
move to numpydoc for doctstrings @adam
update issues templates @adam
Poisson variable gene selection @valentine-svensson
BrainSmallDataset set defualt save_path_10X @gokcen-eraslan
train_size must be float between 0.0 and 1.0 @galen
bump dependency versions @galen
remove reproducibility notebook @galen
fix scanVI dataloading @pierre
0.6.5 (2020-5-10)#
0.6.4 (2020-4-14)#
add back Python 3.6 support @adam
get_sample_scale() allows gene selection @valentine-svensson
bug fix to the dataset to anndata method with how cell measurements are stored @adam
fix requirements @adam
0.6.3 (2020-4-01)#
bug in version for Louvian in setup.py @adam
0.6.2 (2020-4-01)#
update highly variable gene selection to handle sparse matrices @adam
update DE docstrings @pierre
improve posterior save load to also handle subclasses @pierre
Create NB and ZINB distributions with torch and refactor code accordingly @pierre
typos in autozivae @achille
bug in csc sparse matrices in anndata data loader @adam
0.6.1 (2020-3-13)#
0.6.0 (2020-2-28)#
0.5.0 (2019-10-17)#
do not automatically upper case genes @adam
AutoZI @oscar
Made the intro tutorial more user friendly @adam
Tests for LDVAE notebook @adam
fix compatibility issues with sklearn and numba @romain
fix Anndata @francesco-brundu
docstring, totalVI, totalVI notebook and CITE-seq data @adam
fix type @eduardo-beltrame
fixing installation guide @jeff
improved error message for dispersion @stephen-flemming
0.4.1 (2019-08-03)#
0.4.0 (2019-07-25)#
gimVI @achille
synthetic correlated datasets, fixed bug in marginal log likelihood @oscar
autotune, dataset enhancements @gabriel
documentation @jeff
more consistent posterior API, docstring, validation set @adam
fix anndataset @michael-raevsky
linearly decoded VAE @valentine-svensson
support for scanpy, fixed bugs, dataset enhancements @achille
fix filtering bug, synthetic correlated datasets, docstring, differential expression @pierre
better docstring @jamie-morton
classifier based on library size for doublet detection @david-kelley
0.3.0 (2019-05-03)#
corrected notebook @jules
support for batch indices in csvdataset @primoz-godec
speeding up likelihood computations @william-yang
better anndata interop @casey-greene
early stopping based on classifier accuracy @david-kelley
0.2.4 (2018-12-20)#
updated to torch v1 @jules
added stress tests for harmonization @chenling
fixed autograd breaking @romain
make removal of empty cells more efficient @john-reid
switch to os.path.join @casey-greene
0.2.2 (2018-11-08)#
0.2.0 (2018-09-04)#
annotation notebook @eddie
Memory footprint management @jeff
updated early stopping @max
docstring @james-webber
0.1.6 (2018-08-08)#
0.1.5 (2018-07-24)#
0.1.3 (2018-06-22)#
0.1.2 (2018-06-13)#
0.1.0 (2017-09-05)#
First scVI TensorFlow version @romain