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

Bioconductor version: Release (3.18)

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.

Author: Adam Park [aut, cre], Roopali Singh [aut] , Xiang Zhu [aut] , Qunhua Li [aut]

Maintainer: Adam Park <akp6031 at psu.edu>

Citation (from within R, enter citation("retrofit")):


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Retrofit Colon Vignette HTML R Script
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Reference Manual PDF


biocViews Bayesian, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, SingleCell, Software, Spatial, Transcriptomics, Visualization
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2), Rcpp
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URL https://github.com/qunhualilab/retrofit
Bug Reports https://github.com/qunhualilab/retrofit/issues
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