Type: Package
Package: cellNexus
Title: Queries the Human Cell Atlas
Version: 0.99.22
Authors@R: c(
    person(
        "Stefano",
        "Mangiola",
        email = "mangiolastefano@gmail.com",
        role = c("aut", "rev", "ctb"),
        comment = c(ORCID = "0000-0001-7474-836X")
    ),
    person(
        "Mengyuan",
        "Shen",
        email = "shen.m@wehi.edu.au",
        role = c("aut", "cre", "rev"),
        comment = c(ORCID = "0009-0008-0057-8239")
    ),
    person(
        "Michael",
        "Milton",
        email = "milton.m@wehi.edu.au",
        role = c("aut", "rev", "ctb"),
        comment = c(ORCID = "0000-0002-8965-2595")
    ),
    person(
        "Jared",
        "Andrews",
        email = "jared.andrews07@gmail.com",
        role = c("aut", "rev", "ctb")
    ),
    person(
        "Juan",
        "Henao",
        email = "juan.henao@helmholtz-muenchen.de",
        role = c("aut", "ctb")
    ),
    person(
        "Edward",
        "Yang",
        email = "edwardyang125@gmail.com",
        role = c("aut", "ctb")
    ),
    person(
        "Julie",
        "Iskander",
        email = "iskander.j@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 one of several supported formats, including SingleCellExperiment, Seurat,
    or pseudobulk SummarizedExperiment objects. Note: The Human Cell Atlas data
    accessed through this package is subject to its own licensing terms (typically
    Creative Commons Attribution or similar open data licenses as specified by the
    Human Cell Atlas Data Use Agreement), which differ from the package license
    (GPL-3). See the package documentation for details. 
License: GPL-3
Depends: R (>= 4.5.0)
Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>=
        1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, curl,
        cli, SeuratObject, Seurat, methods, rlang, S4Vectors, tibble,
        utils, dbplyr (>= 2.3.0), duckdb, checkmate, shiny,
        shinyWidgets, zellkonverter, anndataR, stringr, Matrix,
        rclipboard
Suggests: BiocStyle, knitr, rmarkdown, testthat, basilisk, arrow,
        reticulate, spelling, forcats, ggplot2, rprojroot, openssl,
        DelayedArray, tidybulk, BiocParallel, preprocessCore
Biarch: true
biocViews: AssayDomain, Infrastructure, SingleCell, RNASeq,
        DifferentialExpression, GeneExpression, Normalization,
        Clustering, QualityControl, Sequencing, Transcription,
        Transcriptomics, ShinyApps
Encoding: UTF-8
RoxygenNote: 7.3.3
URL: https://github.com/MangiolaLaboratory/cellNexus,
        https://mangiolalaboratory.github.io/cellNexus/
BugReports: https://github.com/MangiolaLaboratory/cellNexus/issues
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Collate: 'utils.R' 'counts.R' 'counts_per_million.R' 'data.R' 'dev.R'
        'interface_app.R' 'metadata.R' 'seurat.R' 'unharmonised.R'
        'zzz.R'
Language: en-US
SystemRequirements: Python
NeedsCompilation: no
Packaged: 2026-04-29 03:36:20 UTC; pkgbuild
Author: Stefano Mangiola [aut, rev, ctb] (ORCID:
    <https://orcid.org/0000-0001-7474-836X>),
  Mengyuan Shen [aut, cre, rev] (ORCID:
    <https://orcid.org/0009-0008-0057-8239>),
  Michael Milton [aut, rev, ctb] (ORCID:
    <https://orcid.org/0000-0002-8965-2595>),
  Jared Andrews [aut, rev, ctb],
  Juan Henao [aut, ctb],
  Edward Yang [aut, ctb],
  Julie Iskander [rev],
  Silicon Valley Foundation CZF2019-002443 [fnd],
  NIH NHGRI 5U24HG004059-18 [fnd],
  Victoria Cancer Agency ECRF21036 [fnd],
  NHMRC 1116955 [fnd]
Maintainer: Mengyuan Shen <shen.m@wehi.edu.au>
