Package: GeoTcgaData
Type: Package
Title: Processing Various Types of Data on GEO and TCGA
Version: 2.11.0
Authors@R: person(given = "Erqiang", family = "Hu", email = "13766876214@163.com", role  = c("aut", "cre"), comment = c(ORCID = "0000-0002-1798-7513"))
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) 
    provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP
    and Copy number variation data. It's easy to download data from TCGA using the 
    gdc tool, but processing these data into a format suitable for bioinformatics 
    analysis requires more work. This R package was developed to handle these data.
Depends: R (>= 4.2.0)
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.2.3
Suggests: 
    knitr,
    rmarkdown,
    DESeq2,
    S4Vectors,
    ChAMP,
    impute,
    tidyr,
    clusterProfiler,
    org.Hs.eg.db,
    edgeR,
    limma,
    quantreg,
    minfi,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    dearseq,
    NOISeq,
    testthat (>= 3.0.0),
    CATT,
    TCGAbiolinks,
    enrichplot,
    GEOquery,
    BiocGenerics
VignetteBuilder: knitr
Imports: 
    utils,
    data.table,
    plyr,
    cqn,
    topconfects,
    stats,
    SummarizedExperiment,
    methods
Language: en-US
URL: https://github.com/YuLab-SMU/GeoTcgaData
BugReports: https://github.com/YuLab-SMU/GeoTcgaData/issues
biocViews: GeneExpression, DifferentialExpression, RNASeq, 
	CopyNumberVariation, Microarray, Software, DNAMethylation,
    DifferentialMethylation, SNP, ATACSeq, MethylationArray
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/GeoTcgaData
git_branch: devel
git_last_commit: 4541645
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
