Package: zinbwave
Type: Package
Title: Zero-Inflated Negative Binomial Model for RNA-Seq Data
Version: 1.31.0
Authors@R: 
    c(person("Davide","Risso", role=c("aut","cre", "cph"), 
          email="risso.davide@gmail.com" ),
      person("Svetlana","Gribkova", role="aut", 
          email="svetlana.gribkova@mines-paristech.fr"),
      person("Fanny", "Perraudeau", role="aut",
          email="fperraudeau@berkeley.edu"),
      person("Jean-Philippe", "Vert", role="aut", 
          email="jean-philippe.vert@mines-paristech.fr"),
      person("Clara", "Bagatin", role="aut",
          email="clarabagatin@yahoo.it"))
Description: 
   Implements a general and flexible zero-inflated negative binomial model that
   can be used to provide a low-dimensional representations of single-cell
   RNA-seq data. The model accounts for zero inflation (dropouts), 
   over-dispersion, and the count nature of the data. The model also
   accounts for the difference in library sizes and optionally for batch effects
   and/or other covariates, avoiding the need for pre-normalize the data.
License: Artistic-2.0
Depends: R (>= 3.4), methods, SummarizedExperiment,
        SingleCellExperiment
Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq,
        ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats
VignetteBuilder: knitr
LazyData: TRUE
RoxygenNote: 7.3.1
biocViews: ImmunoOncology, DimensionReduction, GeneExpression, RNASeq,
        Software, Transcriptomics, Sequencing, SingleCell
BugReports: https://github.com/drisso/zinbwave/issues
git_url: https://git.bioconductor.org/packages/zinbwave
git_branch: devel
git_last_commit: c6e6f01
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-04-27
NeedsCompilation: no
Packaged: 2025-04-27 21:56:14 UTC; biocbuild
Author: Davide Risso [aut, cre, cph],
  Svetlana Gribkova [aut],
  Fanny Perraudeau [aut],
  Jean-Philippe Vert [aut],
  Clara Bagatin [aut]
Maintainer: Davide Risso <risso.davide@gmail.com>
Built: R 4.5.0; ; 2025-04-28 02:35:33 UTC; unix
