Type: Package
Package: CuratedAtlasQueryR
Title: Queries the Human Cell Atlas
Version: 1.8.0
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
Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow,
        reticulate, spelling, forcats, ggplot2,
        tidySingleCellExperiment, rprojroot
Biarch: true
biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression,
        GeneExpression, Normalization, Clustering, QualityControl,
        Sequencing, Transcription, Transcriptomics
Encoding: UTF-8
RoxygenNote: 7.2.3
URL: https://github.com/stemangiola/CuratedAtlasQueryR
BugReports: https://github.com/stemangiola/CuratedAtlasQueryR/issues
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Collate: 'utils.R' 'counts.R' 'dev.R' 'metadata.R' 'seurat.R'
        'unharmonised.R' 'zzz.R'
Language: en-US
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:24:15 UTC
RemoteUrl: https://github.com/bioc/CuratedAtlasQueryR
RemoteRef: RELEASE_3_22
RemoteSha: d6fb5dfd42452931af24e731399249f029feaea3
NeedsCompilation: no
Packaged: 2026-01-24 21:18:33 UTC; root
Author: Stefano Mangiola [aut, cre, rev] (ORCID:
    <https://orcid.org/0000-0001-7474-836X>),
  Michael Milton [aut, rev] (ORCID:
    <https://orcid.org/0000-0002-8965-2595>),
  Martin Morgan [ctb, rev],
  Vincent Carey [ctb, rev],
  Julie Iskander [rev],
  Tony Papenfuss [rev],
  Silicon Valley Foundation CZF2019-002443 [fnd],
  NIH NHGRI 5U24HG004059-18 [fnd],
  Victoria Cancer Agency ECRF21036 [fnd],
  NHMRC 1116955 [fnd]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Built: R 4.5.2; ; 2026-01-24 21:26:20 UTC; windows
