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bioc
retrofit:RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
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.
Maintained by Adam Park. Last updated 5 months ago.
transcriptomicsvisualizationrnaseqbayesianspatialsoftwaregeneexpressiondimensionreductionfeatureextractionsinglecellcpp
3 stars 5.08 score 9 scripts