crossmeta

DOI: 10.18129/B9.bioc.crossmeta    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see crossmeta.

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: 3.9

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>

Installation

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

if (!requireNamespace("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")

 

HTML	R Script	crossmeta vignette
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Annotation, BatchEffect, DifferentialExpression, GUI, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription
Version	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 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)
LinkingTo
Suggests	knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	ccmap
Links To Me
Build Report

Package Archives

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

Source Package	crossmeta_1.10.0.tar.gz
Windows Binary	crossmeta_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	crossmeta_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/crossmeta
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/crossmeta
Package Short Url	https://bioconductor.org/packages/crossmeta/
Package Downloads Report	Download Stats