rajewsky-lab / novosparc

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

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)

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)

Read the documentation and the tutorial for more information.