Package: retrofit
Title: RETROFIT: Reference-free deconvolution of cell mixtures in
        spatial transcriptomics
Version: 1.9.0
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: 38c03ca
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-10-07
NeedsCompilation: yes
Packaged: 2025-10-07 23:40:05 UTC; biocbuild
Author: Adam Park [aut, cre],
  Roopali Singh [aut] (ORCID: <https://orcid.org/0000-0001-6539-6622>),
  Xiang Zhu [aut] (ORCID: <https://orcid.org/0000-0003-1134-6413>),
  Qunhua Li [aut] (ORCID: <https://orcid.org/0000-0003-0675-7648>)
Maintainer: Adam Park <akp6031@psu.edu>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-29 17:10:05 UTC; windows
Archs: x64
