Package: HTAN
Type: Package
Title: Query and Retrieve Human Tumor Atlas Network (HTAN) Open-Access
        Data
Version: 0.99.1
Date: 2026-10-14
Authors@R: 
  c(person(given = "Sean",
           family = "Davis",
           role = c("aut", "cre"),
           email = "seandavi@gmail.com",
           comment = c(ORCID = "0000-0002-8991-6458")),
    person(given = "National Cancer Institute",
           role = "fnd",
           comment = "Grant U24CA289073"))
Description: A client for the open-access data of the Human Tumor Atlas
        Network (HTAN), Phase 1. File, biospecimen, clinical and
        provenance metadata are queried locally from a versioned
        parquet snapshot of the ISB-CGC HTAN BigQuery release tables,
        through DuckDB and dbplyr, with no Google account. Open-access
        files are downloaded from the CRDC General Commons (anonymous
        GA4GH DRS) or Synapse (personal access token), and common HTAN
        file formats are read into Bioconductor classes such as
        SingleCellExperiment, SpatialExperiment and
        MultiAssayExperiment.
License: MIT + file LICENSE
URL: https://github.com/seandavi/HTAN, https://seandavi.github.io/HTAN/
BugReports: https://github.com/seandavi/HTAN/issues
Depends: R (>= 4.5.0)
SystemRequirements: Quarto command line tool
        (<https://github.com/quarto-dev/quarto-cli>).
Imports: BiocFileCache, DBI, dbplyr, dplyr, duckdb, httr2, jsonlite,
        methods, MultiAssayExperiment, rlang, S4Vectors,
        SingleCellExperiment, SpatialExperiment, stats,
        SummarizedExperiment, tibble, tools, utils
Suggests: anndataR, BiocIO, ggplot2, knitr, Matrix, quarto, rhdf5,
        scales, scater, scrapper, SeuratObject, TENxIO, tidyr, testthat
        (>= 3.0.0), VisiumIO, withr
biocViews: DataImport, DataRepresentation, BiomedicalInformatics,
        SingleCell, Spatial, ThirdPartyClient, Transcriptomics
VignetteBuilder: quarto
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.1.0
Config/testthat/edition: 3
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-20 11:34:42 UTC
RemoteUrl: https://github.com/BiocStaging/HTAN
RemoteRef: HEAD
RemoteSha: 9efae6be0a2e316df55df7d59f93f7b2c44b39a2
NeedsCompilation: no
Packaged: 2026-10-20 19:36:24 UTC; root
Author: Sean Davis [aut, cre] (ORCID: <https://orcid.org/0000-0002-8991-6458>),
  National Cancer Institute [fnd] (Grant U24CA289073)
Maintainer: Sean Davis <seandavi@gmail.com>