DESCRIPTION

Package: BERLIN
Title: Basic Exploration of Single-Cell RNAseq Data and Lineages
Version: 0.0.0.9000
Authors@R: person("Alyssa", "Obermayer", role = c("aut","cre"),
                     email = "alyssa.obermayer@moffitt.org",
                     comment = c(ORCID = "0000-0002-7333-973X"))
Description: This protocol outlines a comprehensive workflow for analyzing scRNAseq data using R and the Seurat package,
             along with other tools like SeuratDisk, pathwork, dplyr, Single R, and Celldex.
             The protocol covers essential steps such as quality control, normalization, data scaling,
             dimensionality reduction, clustering, and automated cell annotation.
             Following this protocol allows bioinformaticians and researchers to effectively analyze scRNAseq data, identify distinct cell populations,
             and gain valuable insights into cellular dynamics and functions.
             The output files generated by this protocol, including metadata, H5 Seurat files, cell subpopulation metadata, and ISCVA-compliant files,
             facilitate downstream analyses and enable integration with other analysis and visualization tools.
             This protocol provides a standardized and reproducible framework for scRNAseq analysis.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Additional_repositories:
    https://bioconductor.org/packages/release/bioc
Remotes:
    mojaveazure/seurat-disk,
    chris-mcginnis-ucsf/DoubletFinder,
    immunogenomics/presto
Imports:
    dplyr,
    tibble,
    reshape2,
    data.table,
    scales,
    Seurat (>= 5.1.0),
    SeuratObject,
    scGate,
    DoubletFinder,
    SingleR,
    celldex,
    UCell,
    rhdf5,
    BiocParallel,
    Matrix,
    writexl,
    presto,
    fields,
    patchwork,
    BiocManager,
    GenomeInfoDbData,
    SeuratDisk,
    SingleCellExperiment,
    shinycssloaders,
    shiny,
    shinythemes,
    shinyjs,
    shinyjqui,
    pheatmap,
    RColorBrewer,
    umap,
    cowplot,
    ggdendro,
    factoextra,
    viridis,
    readr,
    ggVennDiagram,
    ggtree,
    stringr,
    tools,
    plotly,
    gridExtra,
    tidyverse,
    DT,
    ggplot2,
    ggpubr,
    ggrepel
biocViews:
    scGate,
    UCell,
    SingleR,
    SingleCellExperiment,
    BiocParallel,
    rhdf5,
    GenomeInfoDbData,
    celldex
Depends: 
    R (>= 3.5.0)
LazyData: true
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr