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scArches is a package to integrate newly produced single-cell datasets into integrated references atlases. Our method can facilitate large collaborative projects with decentralise training and integration of multiple datasets by different groups. scArches is compatible with scanpy. and hosts efficient implementations of all conditional generative models for single-cell data.

• Integrate many single-cell datasets and share the trained model and the data (if possible).
• Download a pre-trained model for your atlas of interest, update it wih new datasets and share with your collaborators.
• Project and integrate query datasets on the top of a reference and use latent repesentation for downstream tasks, e.g.: diff testing, clustering.

See here for documentation and tutorials.

If you have a question or new architchuture or a model that could be integrated in to our pipe-line, you can post an issue or reach us by email. Our package support tf/keras now but pytorch version will be added very soon.