Background

Conceptual guides explaining the statistical and algorithmic foundations of scviva-tools models.

• Variational Inference
  • The generative model
  • Gene likelihood
  • Spatial priors (scVIVA, ResolVI)
  • KL annealing
  • References
• Differential Expression
  • Overview
  • Standard DE (vanilla / change mode)
  • Niche DE (scVIVA)
  • Niche abundance DE (ResolVI)
  • References
• Differential Abundance
  • Problem Statement
  • Motivation
  • Notations and model assumptions
  • Quantifying the density of each sample
  • Aggregating posteriors to identify relatively overabundant cell states in a given group of samples
  • Sources
• Spatial Transcriptomics Methods
  • Technology overview
  • Key challenges
  • Neighbour graphs
  • SpatialData integration