DOI: 10.18129/B9.bioc.crossmeta  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see crossmeta.

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: 3.16

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 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.

Author: Alex Pickering

Maintainer: Alex Pickering <alexvpickering at>

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


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


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HTML R Script crossmeta vignette
PDF   Reference Manual


biocViews Annotation, BatchEffect, DifferentialExpression, GUI, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription
Version 1.24.0
In Bioconductor since BioC 3.4 (R-3.3) (6.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
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), DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), edgeR, fdrtool (>= 1.2.15), GEOquery(>= 2.40.0), limma(>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), miniUI (>= 0.1.1), methods, oligo(>= 1.38.0), reader (>= 1.0.6), RCurl (>=, RSQLite (>= 2.1.1), stringr (>= 1.2.0), sva(>= 3.22.0), shiny (>= 1.0.0), shinyjs (>= 2.0.0), shinyBS (>= 0.61), shinyWidgets (>= 0.5.3), shinypanel (>= 0.1.0), tibble, XML (>=, readxl (>= 1.3.1)
Suggests knitr, rmarkdown, lydata,, testthat
SystemRequirements libxml2: libxml2-dev (deb), libxml2-devel (rpm) libcurl: libcurl4-openssl-dev (deb), libcurl-devel (rpm) openssl: libssl-dev (deb), openssl-devel (rpm), libssl_dev (csw), openssl@1.1 (brew)
Depends On Me
Imports Me
Suggests Me ccmap
Links To Me
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Source Package crossmeta_1.24.0.tar.gz
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