The supporting Python package of SAVER-X
One can also use this Python package for pre-training using public data. Instructions on pre-training will come out soon.
pip install sctransfer
The package only supports Python (>=3.5).
Update: the package now works with tensorflow 2
Update: the package requires tensorflow version <=2.2.0 and keras version <=2.3.0.
Update: the package has been updated to work with the newer version of scanpy.
To test whether the installation is successful or not, you can try with the following code. The mtx file for testing can be downloaded here
import sctransfer.api as api api.autoencode(mtx_file = "shekhar_downsampled.mtx")