Package: AnnotatedBCGEData
Title: 100+ Curated Breast Cancer Gene Expression Data sets
Version: 0.99.13
Date: 2025-10-16
Authors@R: 
    c(person("Heidi", "Steadman", 
        email = "hstead05@byu.edu", 
        role = "aut"), 
    person("Shu-Fei", "Lo", 
        email = "shufeilo@byu.edu", 
        role = "aut"),
    person("Stephen", "Piccolo", 
        email = "stephen_piccolo@byu.edu", 
        role = c("cre", "aut"),
        comment = c(ORCID = "0000-0003-2001-5640")),
    person("BYU", "College Undergraduate Research Award",
        role = "fnd")
    )
Description: AnnotatedBCGEData is an R Bioconductor package that
        provides access to more than 100 gene-expression datasets
        generated using microarray and RNA- sequencing technologies. We
        collected these datsets from public repositories, including
        Gene Expression Omnibus, ArrayExpress, and The Cancer Genome
        Atlas. Where feasible, we obtained and reprocessed the raw data
        using computational pipelines and annotations that were
        standardized and more updated than those used to process the
        data originally. Additionally, we annotated the sample metadata
        using oncology terms from the National Cancer Institute
        Thesaurus. This was necessary because different data submitters
        used different terminology to describe breast-cancer patients
        and samples. Mapping the metadata to ontology terms makes it
        possible for users to search the data using these standardized
        terms.
License: CC0
URL: https://github.com/srp33/AnnotatedBCGEData
BugReports: https://github.com/srp33/AnnotatedBCGEData//issues
biocViews: ExperimentData, CancerData, ExpressionData,
        Homo_sapiens_Data, GEO, ArrayExpress, Tissue, MicroarrayData,
        SequencingData, BreastCancerData, Genome, TissueMicroarrayData
Encoding: UTF-8
Roxygen: list(markdown=TRUE)
Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, ggplot2, testthat
        (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 4.5)
Imports: SummarizedExperiment, stringr, readr, dplyr, tibble, tidyr,
        zen4R, BiocFileCache, cli, rlang, readxl
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libicu-dev libsecret-1-dev libxml2-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-22 21:58:40 UTC
RemoteUrl: https://github.com/bioc/AnnotatedBCGEData
RemoteRef: HEAD
RemoteSha: 3f5c4dff869df3e210ecae89a24e1e25b81857d7
NeedsCompilation: no
Packaged: 2026-10-23 08:23:06 UTC; root
Author: Heidi Steadman [aut],
  Shu-Fei Lo [aut],
  Stephen Piccolo [cre, aut] (ORCID:
    <https://orcid.org/0000-0003-2001-5640>),
  BYU College Undergraduate Research Award [fnd]
Maintainer: Stephen Piccolo <stephen_piccolo@byu.edu>