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

BEAR Apps Version

2021b

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

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