To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("crossmeta")

In most cases, you don't need to download the package archive at all.

crossmeta

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see crossmeta.

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: 3.4

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.

Author: Alex Pickering

Maintainer: Alex Pickering <alexvpickering at gmail.com>

Citation (from within R, enter citation("crossmeta")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("crossmeta")

Documentation

HTML R Script crossmeta vignette

PDF Reference Manual

Text LICENSE

Details

biocViews Annotation, BatchEffect, DifferentialExpression, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription

Version 1.0.1

In Bioconductor since BioC 3.4 (R-3.3) (0.5 years)

License MIT + file LICENSE

Depends R (>= 3.3)

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)

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