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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
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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 |
| 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) |
| 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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