novosparc

De novo spatial reconstruction of single-cell gene expression.

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novoSpaRc - de novo Spatial Reconstruction of Single-Cell Gene Expression

.. image:: https://raw.githubusercontent.com/nukappa/nukappa.github.io/master/images/novosparc.png :width: 90px :align: left

novoSpaRc predicts locations of single cells in space by solely using single-cell RNA sequencing data. An existing reference database of marker genes is not required, but significantly enhances performance if available.

novoSpaRc accompanies the following publications:

| *Gene Expression Cartography*
| M Nitzan*, N Karaiskos*, N Friedman†, N Rajewsky†
| `Nature (2019) <https://www.nature.com/articles/s41586-019-1773-3>`_

and

| *novoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport*
| N Moriel*, E Senel*, N Friedman, N Rajewsky, N Karaiskos†, M Nitzan†
| `Nature Protocols (2021) <https://www.nature.com/articles/s41596-021-00573-7>`_

Read the documentation <https://novosparc.readthedocs.io> and the tutorial <https://github.com/rajewsky-lab/novosparc/blob/master/reconstruct_drosophila_embryo_tutorial.ipynb> for more information.

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