retrofit
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
Bioconductor version: Release (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("retrofit")
):
Installation
To install this package, start R (version "4.4") 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")
Retrofit Colon Vignette | HTML | R Script |
Retrofit Simulation Vignette | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Bayesian, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, SingleCell, Software, Spatial, Transcriptomics, Visualization |
Version | 1.4.0 |
In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
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_1.4.0.tar.gz |
Windows Binary | retrofit_1.4.0.zip (64-bit only) |
macOS Binary (x86_64) | retrofit_1.4.0.tgz |
macOS Binary (arm64) | retrofit_1.4.0.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 |