DESCRIPTION

Package: scFlow
Title: A Single-Cell/Nuclei Analysis Toolkit
Version: 0.7.4
Authors@R: 
    c(
    person(given = "Combiz",
           family = "Khozoie",
           role = c("aut", "cre"),
           email = "c.khozoie@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-1634-5287")),
    person(given = "Nurun",
           family = "Fancy",
           role = c("aut"),
           email = "n.fancy@imperial.ac.uk",
           comment = c(ORCID = "0000-0002-6481-6266")),
    person(given = "Mahdi",
           family = "Marjaneh",
           role = c("aut"),
           email = "m.moradi@imperial.ac.uk",
           comment = c(ORCID = "YOUR-ORCID-ID")),
    person(given = "Michael",
           family = "Thomas",
           role = c("aut"),
           email = "michael.thomas21@imperial.ac.uk",
           comment = c(ORCID = "YOUR-ORCID-ID")),       
    person(given = "Nathan",
           family = "Skene",
           role = c("aut"),
           email = "n.skene@imperial.ac.uk",
           comment = c(ORCID = "YOUR-ORCID-ID"))
    )
Description: Single-cell/nuclei RNA-seq analysis tools in R to build a complete analysis workflow.
Roxygen: list(markdown = TRUE)
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/combiz/scFlow
BugReports: https://github.com/combiz/scFlow/issues
Suggests: 
    testthat (>= 2.1.0),
    spelling,
    covr,
    knitr,
    BiocStyle,
    DT (>= 0.26)
Language: en-US
RoxygenNote: 7.3.1
biocViews:
Imports: 
    Matrix,
    assertthat (>= 0.2.1),
    bib2df,
    biomaRt (>= 2.54.0),
    cli (>= 3.4.1),
    cowplot (>= 1.1.1),
    DirichletReg (>= 0.7.1),
    dplyr (>= 1.1.0),
    DoubletFinder (>= 2.0.3),
    DropletUtils (>= 1.18.1),
    edgeR (>= 3.40.0),
    english (>= 1.2.6),
    enrichR (>= 3.1),
    EWCE (>= 1.6.0),
    forcats (>= 0.5.2),
    formattable (>= 0.2.1),
    future (>= 1.29.0),
    future.apply (>= 1.10.0),
    ggdendro (>= 0.1.23),
    ggplot2 (>= 3.4.0),
    ggpubr (>= 0.5.0),
    ggrepel (>= 0.9.2),
    ggridges (>= 0.5.4),
    kBET (>= 0.99.6),
    leaflet (>= 2.1.1),
    limma (>= 3.54.0),
    magrittr (>= 2.0.3),
    MAST (>= 1.24.0),
    methods,
    monocle3 (>= 1.3.1),
    paletteer (>= 1.5.0),
    patchwork,
    plotly,
    plyr (>= 1.8.8),
    preprocessCore,
    purrr (>= 0.3.5),
    qs,
    R.utils,
    rlang (>= 1.0.6),
    rliger,
    rmarkdown (>= 2.18),
    Rtsne (>= 0.16),
    scales,
    scater (>= 1.26.1),
    sctransform,
    Seurat (>= 4.3.0),
    SingleCellExperiment (>= 1.20.0),
    stringr (>= 1.4.1),
    SummarizedExperiment (>= 1.28.0),
    threejs (>= 0.3.3),
    tibble (>= 3.1.8),
    tidyr (>= 1.2.1),
    tidyselect (>= 1.2.0),
    UpSetR (>= 1.4.0),
    utils (>= 4.2.1),
    uwot,
    WebGestaltR
Remotes:
    NathanSkene/EWCE,
    chris-mcginnis-ucsf/DoubletFinder,
    ropensci/plotly,
    cole-trapnell-lab/monocle3,
    theislab/kBET,
    jlmelville/uwot,
    ropensci/bib2df
VignetteBuilder: knitr