crossmeta

DOI: 10.18129/B9.bioc.crossmeta  

This is the development version of crossmeta; for the stable release version, see crossmeta.

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: Development (3.18)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("crossmeta")

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

Documentation

PDF		Reference Manual

Details

biocViews	Annotation, BatchEffect, DifferentialExpression, GUI, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription
Version	1.27.0
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 (>= 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)
LinkingTo
Suggests	knitr, rmarkdown, lydata, org.Hs.eg.db, 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)
Enhances
URL	https://github.com/alexvpickering/crossmeta
BugReports	https://github.com/alexvpickering/crossmeta/issues
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
Windows Binary	crossmeta_1.27.0.zip
macOS Binary (x86_64)	crossmeta_1.27.0.tgz
macOS Binary (arm64)
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