This is the development version of retrofit; for the stable release version, see retrofit.
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomicsBioconductor version: Development (3.22)
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] ORCID: 0000-0001-6539-6622 , Xiang Zhu [aut] ORCID: 0000-0003-1134-6413 , Qunhua Li [aut] ORCID: 0000-0003-0675-7648
Maintainer: Adam Park <akp6031 at psu.edu>
Citation (from within R, entercitation("retrofit")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("retrofit")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("retrofit")Follow Installation instructions to use this package in your R session.
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