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
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:22:56 UTC
RemoteUrl: https://github.com/bioc/retrofit
RemoteRef: HEAD
RemoteSha: 88f4e91d5d33b4ecf5df0cd8258c5193109ab93a
NeedsCompilation: yes
Packaged: 2026-01-26 08:14:52 UTC; root
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; aarch64-apple-darwin23; 2026-01-26 08:16:53 UTC; unix
