DOI: 10.18129/B9.bioc.retrofit  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see retrofit.

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

Bioconductor version: 3.17

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>

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biocViews Bayesian, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, SingleCell, Software, Spatial, Transcriptomics, Visualization
Version 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
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