Package: Dino
Type: Package
Title: Normalization of Single-Cell mRNA Sequencing Data
Version: 1.16.0
Authors@R: c(
    person("Jared", "Brown", email = "brownj@ds.dfci.harvard.edu",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9151-4386")),
    person("Christina", "Kendziorski", role= c("ctb")))
biocViews: Software, Normalization, RNASeq, SingleCell, Sequencing,
        GeneExpression, Transcriptomics, Regression, CellBasedAssays
Description: Dino normalizes single-cell, mRNA sequencing data to
        correct for technical variation, particularly sequencing depth,
        prior to downstream analysis. The approach produces a matrix of
        corrected expression for which the dependency between
        sequencing depth and the full distribution of normalized
        expression; many existing methods aim to remove only the
        dependency between sequencing depth and the mean of the
        normalized expression. This is particuarly useful in the
        context of highly sparse datasets such as those produced by 10X
        genomics and other uninque molecular identifier (UMI) based
        microfluidics protocols for which the depth-dependent
        proportion of zeros in the raw expression data can otherwise
        present a challenge.
Depends: R (>= 4.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.1
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools,
        ggplot2, gridExtra, ggpubr, grid, magick, hexbin
VignetteBuilder: knitr
Imports: BiocParallel, BiocSingular, SummarizedExperiment,
        SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats,
        parallel, scran, grDevices, stats, methods
URL: https://github.com/JBrownBiostat/Dino
BugReports: https://github.com/JBrownBiostat/Dino/issues
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:10:41 UTC
RemoteUrl: https://github.com/bioc/Dino
RemoteRef: RELEASE_3_22
RemoteSha: 479c99380f055f2344084fbe3f4441cb8dc911b4
NeedsCompilation: no
Packaged: 2025-11-11 14:03:39 UTC; root
Author: Jared Brown [aut, cre] (ORCID: <https://orcid.org/0000-0002-9151-4386>),
  Christina Kendziorski [ctb]
Maintainer: Jared Brown <brownj@ds.dfci.harvard.edu>
Built: R 4.5.2; ; 2025-11-11 14:13:38 UTC; windows
