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

 

   

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: Release (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) (< 6 months)
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)
LinkingTo
Suggests knitr, rmarkdown, lydata, org.Hs.eg.db, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me ccmap
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source crossmeta_1.0.1.tar.gz
Windows Binary crossmeta_1.0.1.zip
Mac OS X 10.9 (Mavericks) crossmeta_1.0.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/crossmeta/tree/release-3.4
Package Short Url http://bioconductor.org/packages/crossmeta/
Package Downloads Report Download Stats

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