Package: retrofit
Title: RETROFIT: Reference-free deconvolution of cell mixtures in spatial 
    transcriptomics
Version: 1.11.0
Authors@R:
    c(person(given = "Adam",
           family = "Park",
           role = c("aut","cre"),
           email = "akp6031@psu.edu",
           comment = c()),
      person(given = "Roopali",
           family = "Singh",
           role = c("aut"),
           email = "rus82@psu.edu",
           comment = c(ORCID = "0000-0001-6539-6622")),
      person(given = "Xiang",
           family = "Zhu",
           role = c("aut"),
           email = "xiangzhu@psu.edu",
           comment = c(ORCID = "0000-0003-1134-6413")),
      person(given = "Qunhua",
           family = "Li",
           role = c("aut"),
           email = "qunhua.li@psu.edu",
           comment = c(ORCID = "0000-0003-0675-7648"))
    )
Description: 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. 
biocViews: Transcriptomics, Visualization, RNASeq, Bayesian, Spatial, Software,
    GeneExpression, DimensionReduction, FeatureExtraction, SingleCell
License: GPL-3
Encoding: UTF-8
LazyData: FALSE
URL: https://github.com/qunhualilab/retrofit
BugReports: https://github.com/qunhualilab/retrofit/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends:
    R (>= 4.2),
    Rcpp
LinkingTo: 
    Rcpp
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    testthat,
    DescTools,
    ggplot2,
    corrplot,
    cowplot,
    grid,
    colorspace,
    png,
    reshape2,
    pals,
    RCurl
VignetteBuilder:
    knitr
git_url: https://git.bioconductor.org/packages/retrofit
git_branch: devel
git_last_commit: 88f4e91
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
