DESCRIPTION

Type: Package
Package: CuratedAtlasQueryR
Title: Queries the Human Cell Atlas
Version: 1.4.7
Authors@R: c(
    person(
        "Stefano",
        "Mangiola",
        email = "mangiolastefano@gmail.com",
        role = c("aut", "cre", "rev"),
        comment = c(ORCID = "0000-0001-7474-836X")
    ),
    person(
        "Michael",
        "Milton",
        email = "milton.m@wehi.edu.au",
        role = c("aut", "rev"),
        comment = c(ORCID = "0000-0002-8965-2595")
    ),
    person(
        "Martin",
        "Morgan",
        email = "Martin.Morgan@RoswellPark.org",
        role = c("ctb", "rev")
    ),
    person(
        "Vincent",
        "Carey",
        email = "stvjc@channing.harvard.edu",
        role = c("ctb", "rev")
    ),
    person(
        "Julie",
        "Iskander",
        email = "iskander.j@wehi.edu.au",
        role = c( "rev")
    ),
    person(
        "Tony",
        "Papenfuss",
        email = "papenfuss@wehi.edu.au",
        role = c( "rev")
    ),
    person(
        "Silicon Valley Foundation",
        "CZF2019-002443",
        role = c( "fnd")
    ),
    person(
        "NIH NHGRI",
        "5U24HG004059-18",
        role = c( "fnd")
    ),
    person(
        "Victoria Cancer Agency",
        "ECRF21036",
        role = c( "fnd")
    ),
    person(
        "NHMRC",
        "1116955",
        role = c( "fnd")
    ))
Description: Provides access to a copy of the Human Cell Atlas, but with 
    harmonised metadata. This allows for uniform querying across numerous 
    datasets within the Atlas using common fields such as cell type, tissue 
    type, and patient ethnicity. Usage involves first querying the metadata
    table for cells of interest, and then downloading the corresponding cells 
    into a SingleCellExperiment object. 
License: GPL-3
Depends:
    R (>= 4.2.0)
Imports:
    dplyr,
    SummarizedExperiment,
    SingleCellExperiment,
    purrr (>= 1.0.0),
    BiocGenerics,
    glue,
    HDF5Array,
    DBI,
    tools,
    httr,
    cli,
    assertthat,
    SeuratObject,
    Seurat,
    methods,
    rlang,
    stats,
    S4Vectors,
    tibble,
    utils,
    dbplyr (>= 2.3.0),
    duckdb,
    stringr,
    checkmate,
    stringfish
Suggests:
    zellkonverter,
    rmarkdown,
    knitr,
    testthat,
    basilisk,
    arrow,
    reticulate,
    spelling,
    forcats,
    ggplot2,
    tidySingleCellExperiment,
    rprojroot,
    openssl,
    scuttle,
    DelayedArray
Biarch: true
biocViews: 
    AssayDomain,
    Infrastructure,
    RNASeq,
    DifferentialExpression,
    GeneExpression,
    Normalization,
    Clustering,
    QualityControl,
    Sequencing,
    Transcription,
    Transcriptomics
Encoding: UTF-8
RoxygenNote: 7.3.2
LazyDataCompression: xz
URL: https://github.com/stemangiola/CuratedAtlasQueryR
BugReports: https://github.com/stemangiola/CuratedAtlasQueryR/issues
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Collate: 
    'utils.R'
    'counts.R'
    'counts_per_million.R'
    'data.R'
    'dev.R'
    'import_metadata_and_counts.R'
    'metadata.R'
    'seurat.R'
    'unharmonised.R'
    'zzz.R'
Language: en-US
LazyData: true