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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | retrofit_1.13.0.zip |
| macOS Binary (big-sur-x86_64) | retrofit_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | retrofit_1.13.0.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 |