DESCRIPTION

Package: zinbwave
Type: Package
Title: Zero-Inflated Negative Binomial Model for RNA-Seq Data
Version: 1.9.1
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,
    Seurat
VignetteBuilder: knitr
LazyData: TRUE
RoxygenNote: 6.1.1
biocViews: ImmunoOncology, 
  DimensionReduction,
  GeneExpression,
  RNASeq,
  Software,
  Transcriptomics,
  Sequencing,
  SingleCell
BugReports: https://github.com/drisso/zinbwave/issues