crossmeta

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see crossmeta.

Cross Platform Meta-Analysis of Microarray Data


Bioconductor version: 3.10

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/pathway 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. Finally, effect size and pathway meta-analyses can proceed and the results graphically explored.

Author: Alex Pickering

Maintainer: Alex Pickering <alexvpickering at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crossmeta")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("crossmeta")
crossmeta vignette HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Annotation, BatchEffect, DifferentialExpression, GUI, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription
Version 1.12.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License MIT + file LICENSE
Depends R (>= 3.5)
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), ccmap, DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), doParallel (>= 1.0.10), doRNG (>= 1.6), foreach (>= 1.4.3), fdrtool (>= 1.2.15), ggplot2 (>= 2.2.1), GEOquery(>= 2.40.0), limma(>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), metap (>= 0.8), miniUI (>= 0.1.1), oligo(>= 1.38.0), plotly (>= 4.5.6), reshape (>= 0.8.6), reader (>= 1.0.6), RColorBrewer (>= 1.1.2), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), rdrop2 (>= 0.7.0), stringr (>= 1.2.0), sva(>= 3.22.0), shiny (>= 1.0.0), stats (>= 3.3.3), XML (>= 3.98.1.17)
System Requirements
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Suggests knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata
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Package Archives

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

Source Package crossmeta_1.12.0.tar.gz
Windows Binary crossmeta_1.12.0.zip
Mac OS X 10.11 (El Capitan) crossmeta_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/crossmeta
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crossmeta
Bioc Package Browser https://code.bioconductor.org/browse/crossmeta/
Package Short Url https://bioconductor.org/packages/crossmeta/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive