Package: retrofit 1.5.0

Adam Park

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.

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

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On BioConductor:retrofit-1.5.0(bioc 3.20)retrofit-1.4.0(bioc 3.19)

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Last updated 2 months agofrom:7dc1ce2cfe

Exports:annotateWithCorrelationsannotateWithMarkersdecomposeretrofit

Dependencies:Rcpp