retrofit

RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics

Bioconductor version: 3.23 · Package version: 1.12.0

RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("retrofit")