NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics data.

ABSTRACT:

Motivation

Spatial transcriptomics (ST) can reveal the existence and extent of spatial variation of gene expression in complex tissues. Such analyses could help identify spatially localized processes underlying a tissue's function. Existing tools to detect spatially variable genes assume a constant noise variance across spatial locations. This assumption might miss important biological signals when the variance can change across locations.

Results

In this article, we propose NoVaTeST, a framework to identify genes with location-dependent noise variance in ST data. NoVaTeST models gene expression as a function of spatial location and allows the noise to vary spatially. NoVaTeST then statistically compares this model to one with constant noise and detects genes showing signifi

SUBMITTER: Abrar MA 

PROVIDER: S-EPMC10283152 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature