crossmeta

This is the released version of crossmeta; for the devel version, see crossmeta.

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: Release (3.20)

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") 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


Reference Manual	PDF
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, BatchEffect, DifferentialExpression, GUI, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription
Version	1.31.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 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 (>= 1.95.4.11), 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 (>= 3.98.1.17), readxl (>= 1.3.1)
System Requirements	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)
URL	https://github.com/alexvpickering/crossmeta
Bug Reports	https://github.com/alexvpickering/crossmeta/issues

Suggests	knitr, rmarkdown, lydata, org.Hs.eg.db, testthat
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)	crossmeta_1.31.0.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