Published April 20, 2021 | Version v0.4.3
Software Open

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

Authors/Creators

  • 1. The Hebrew University of Jerusalem
  • 2. Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association

Description

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 publication:

Gene Expression Cartography

M. Nitzan, N. Karaiskos, N. Friedman, N. Rajewsky

Nature (2019)

Files

novosparc-0.4.3.zip

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Additional details

Related works

Is supplement to
https://github.com/rajewsky-lab/novosparc/tree/v0.4.3 (URL)

References

  • Nitzan, Mor, et al. "Gene expression cartography." Nature 576.7785 (2019): 132-137.