Package: crossmeta
Title: Cross Platform Meta-Analysis of Microarray Data
Version: 1.0.1
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. A user
    interface makes it easy to select control and treatment samples for each
    contrast and study. This input is used for subsequent surrogate variable
    analysis (models unaccounted sources of variation) and differential
    expression analysis. Final meta-analysis of differential expression values can
    include genes measured in only a subset of studies.
Depends: R (>= 3.3)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 5.0.1
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat
Imports: affy (>= 1.50.0), affxparser (>= 1.44.0), AnnotationDbi (>=
        1.34.4), Biobase (>= 2.32.0), BiocGenerics (>= 0.18.0),
        BiocInstaller (>= 1.22.3), DT (>= 0.2), data.table (>= 1.9.6),
        fdrtool (>= 1.2.15), GEOquery (>= 2.38.4), limma (>= 3.28.17),
        matrixStats (>= 0.50.2), metaMA (>= 3.1.2), miniUI (>= 0.1.1),
        oligo (>= 1.36.1), pander (>= 0.6.0), RColorBrewer (>= 1.1.2),
        rdrop2 (>= 0.7.0), stringr (>= 1.0.0), sva (>= 3.20.0), shiny
        (>= 0.13.2)
biocViews: GeneExpression, Transcription, DifferentialExpression,
        Microarray, TissueMicroarray, OneChannel, Annotation,
        BatchEffect, Preprocessing
NeedsCompilation: no
Packaged: 2016-11-27 01:30:37 UTC; biocbuild
Built: R 3.3.2; ; 2016-11-27 02:51:13 UTC; windows
