retrofit
This is thereleased version of retrofit; for the devel version, seeretrofit.
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
Bioconductor version: Release (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("retrofit")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("retrofit")For older versions of R, please refer to the appropriateBioconductor 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 | 1.10.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | retrofit_1.10.0.tar.gz |
| Windows Binary (x86_64) | retrofit_1.10.0.zip |
| macOS Binary (x86_64) | retrofit_1.10.0.tgz |
| macOS Binary (arm64) | retrofit_1.10.0.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 |