This GitHub repository contains the implementation of Sobolev Alignment, a computational framework designed to align pre-clinical and tumor scRNA-seq data. Sobolev Alignment combines a deep generative model with a kernel method to detect non-linear processes that are shared by a source (e.g., cell line) and a target (e.g., tumor) dataset.
Please refer to the documentation. In particular, the
You need to have Python 3.8 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.
The installation can be done in two steps.
You can install Sobolev Alignment and (almost) all dependencies using the following command:
pip install sobolev-alignment
The resulting package is ready to use, but will use scikit-learn instead of Falkon, resulting in largely sub-optimal performances.
To employ large-scale GPU-accelerated kernel methods, we turn to Falkon. The installation notice for Falkon is available on the FalkonML documentation. The previous installation procedure has already taken care of the various dependencies required for Falkon (i.e., cython, scipy and torch.)
In the folder tutorial
, you will find different tutorial in the form of Jupyter notebooks examplifying how to use the package. Specifically:
an.layers['counts'] = an.X
.Additional packages need to be installed to use MNN on top of Sobolev Alignment:
pip install rpy2
).BiocManager::install("batchelor") '''
Due to incompatibilities between g++, gcc and cuda, the installation of FalkonML sometimes fails. The following elements can help alleviate potential issues:
For Mac users, the jaxlib version installed from PyPI sometimes returns issues. We then advise to re-install jaxlib from condo, and subsequently re-install dcvi-tools:
mamba install jaxlib
mamba install scvi-tools
Errors are sometimes raised due to numba inconsistencies. The errors raised were due to clashes between different packages. Re-installing numba seem to have fixed the issues:
pip install numba --force-reinstall
Please feel free to contact the development team by e-mail or by creating an issue.
See the changelog.
For questions and help requests, you can reach out at the following e-mail address: s [dot] mourragui [at] hubrecht [dot] eu.
If you find this package useful, please cite our publication: