Welcome to CellRegMap’s documentation!
What is CellRegMap
The cellular regulatory map (cellregmap) is a statistical framework to map context-specific effects of genetic variants on single-cell gene expression.
It builds on a linear mixed model and is implemented in Python.
What do you need to run CellRegMap
Single-cell expression profiles assayed through scRNA-seq in the form of a count matrix (cells x genes)
Cellular contexts: these can be known factors or a latent representation of the space (e.g., PCs by cells)
Genotypes: CellRegMap tests for individual eQTL effects between a genetic variant and a gene’s expression, so genotypes need to be provided for variants of interest.
A kinship matrix accounting for relatedness among samples.