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

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 03 Apr 2021Publisher:Zenodo
Authors: Noa Moriel; Enes Senel; Nir Friedman; Nikolaus Rajewsky; Nikos Karaiskos; Mor Nitzan;
Code repository: https://github.com/rajewsky-lab/novosparc/tree/v0.4.2

doi: 10.5281/zenodo.4661200 , 10.5281/zenodo.4705267 , 10.5281/zenodo.4661199 , 10.5281/zenodo.4705325

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

Abstract

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)

{"references": ["Nitzan, Mor, et al. \"Gene expression cartography.\" Nature 576.7785 (2019): 132-137."]}

Related Organizations
Keywords

Spatial transcriptomics, Optimal transport, Single-cell reconstruction, Single-cell RNA-seq

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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