SpaTalk 1.0-foss-2021b-R-4.2.0

A spatially resolved cell-cell communication inference method relying on the graph network and knowledge graph to model ligand-receptor-target signaling network between the spatially proximal cells, which were decomposed from the ST data through the non-negative linear model and spatial mapping between single-cell RNA-seq and ST data. SpaTalk is a reliable method that can help scientists uncover the spatially resolved cell-cell communications for either single-cell or spot-based ST data universally, providing new insights into the understanding of spatial cellular dynamics in tissues.

Accessing SpaTalk 1.0-foss-2021b-R-4.2.0

To load the module for SpaTalk 1.0-foss-2021b-R-4.2.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load SpaTalk/1.0-foss-2021b-R-4.2.0

BEAR Apps Version

2020a

Extensions

  • ggalluvial 0.12.3
  • ggfun 0.0.6
  • NNLM 0.4.3
  • scatterpie 0.1.7
  • SpaTalk 1.0

More Information

For more information visit the SpaTalk website.

Dependencies

This version of SpaTalk has a direct dependency on: foss/2021b R/4.2.0-foss-2021b R-bundle-Bioconductor/3.15-foss-2021b-R-4.2.0

Required By

This version of SpaTalk is a direct dependent of: BEAR-R-bio/2021b-foss-2021b-R-4.2.0

Last modified on 11th August 2022