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 (3.21)
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:
Maintainer: Adam Park <akp6031 at psu.edu>
citation("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.
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 | 1.7.0 |
| 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | retrofit_1.7.0.zip |
| macOS Binary (x86_64) | retrofit_1.7.0.tgz |
| macOS Binary (arm64) | retrofit_1.7.0.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 |