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retrofit

This is the development version of retrofit; for the stable release version, see retrofit.

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


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("retrofit")
Retrofit Colon Vignette HTML R Script
Retrofit Simulation Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, SingleCell, Software, Spatial, Transcriptomics, Visualization
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2), Rcpp
Imports
System Requirements
URL https://github.com/qunhualilab/retrofit
Bug Reports https://github.com/qunhualilab/retrofit/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package retrofit_1.3.0.tar.gz
Windows Binary retrofit_1.3.0.zip
macOS Binary (x86_64) retrofit_1.3.0.tgz
macOS Binary (arm64) retrofit_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/retrofit
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/retrofit
Bioc Package Browser https://code.bioconductor.org/browse/retrofit/
Package Short Url https://bioconductor.org/packages/retrofit/
Package Downloads Report Download Stats