Package: Dino
Type: Package
Title: Normalization of Single-Cell mRNA Sequencing Data
Version: 1.6.0
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
git_url: https://git.bioconductor.org/packages/Dino
git_branch: RELEASE_3_17
git_last_commit: efa6351
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-25 20:55:30 UTC; biocbuild
Author: Jared Brown [aut, cre] (<https://orcid.org/0000-0002-9151-4386>),
  Christina Kendziorski [ctb]
Maintainer: Jared Brown <brownj@ds.dfci.harvard.edu>
Built: R 4.3.1; ; 2023-07-17 12:38:24 UTC; unix
