Package: crossmeta
Title: Cross Platform Meta-Analysis of Microarray Data
Version: 1.30.0
Author: Alex Pickering
Maintainer: Alex Pickering <alexvpickering@gmail.com>
Description: Implements cross-platform and cross-species meta-analyses of Affymentrix,
    Illumina, and Agilent microarray data. This package automates common tasks
    such as downloading, normalizing, and annotating raw GEO data. The user then
    selects control and treatment samples in order to perform differential
    expression analyses for all comparisons. After analysing each contrast
    seperately, the user can select tissue sources for each contrast and specify
    any tissue sources that should be grouped for the subsequent meta-analyses.
Depends: R (>= 4.0)
SystemRequirements: libxml2: libxml2-dev (deb), libxml2-devel (rpm)
        libcurl: libcurl4-openssl-dev (deb), libcurl-devel (rpm)
        openssl: libssl-dev (deb), openssl-devel (rpm), libssl_dev
        (csw), openssl@1.1 (brew)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 7.1.2
VignetteBuilder: knitr
URL: https://github.com/alexvpickering/crossmeta
BugReports: https://github.com/alexvpickering/crossmeta/issues
Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat
Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>=
        1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0),
        BiocManager (>= 1.30.4), DT (>= 0.2), DBI (>= 1.0.0),
        data.table (>= 1.10.4), edgeR, fdrtool (>= 1.2.15), GEOquery
        (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0),
        metaMA (>= 3.1.2), miniUI (>= 0.1.1), methods, oligo (>=
        1.38.0), reader(>= 1.0.6), RCurl (>= 1.95.4.11), RSQLite (>=
        2.1.1), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0),
        shinyjs (>= 2.0.0), shinyBS (>= 0.61), shinyWidgets (>= 0.5.3),
        shinypanel (>= 0.1.0), tibble, XML (>= 3.98.1.17), readxl (>=
        1.3.1)
biocViews: GeneExpression, Transcription, DifferentialExpression,
        Microarray, TissueMicroarray, OneChannel, Annotation,
        BatchEffect, Preprocessing, GUI
git_url: https://git.bioconductor.org/packages/crossmeta
git_branch: RELEASE_3_19
git_last_commit: 7500c56
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-01 22:04:46 UTC; biocbuild
Built: R 4.4.0; ; 2024-05-02 12:39:37 UTC; windows
