retrofit

DOI: 10.18129/B9.bioc.retrofit  

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

Bioconductor version: Release (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 psu.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	Retrofit Colon Vignette
HTML	R Script	Retrofit Simulation Vignette
PDF		Reference Manual
Text		NEWS

Details

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)
License	GPL-3
Depends	R (>= 4.2), Rcpp
Imports
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl
SystemRequirements
Enhances
URL	https://github.com/qunhualilab/retrofit
BugReports	https://github.com/qunhualilab/retrofit/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	retrofit_1.0.0.tar.gz
Windows Binary	retrofit_1.0.0.zip
macOS Binary (x86_64)	retrofit_1.0.0.tgz
macOS Binary (arm64)	retrofit_1.0.0.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
Old Source Packages for BioC 3.17	Source Archive