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>
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 | ||
| LICENSE | Text |
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) (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 | |
| URL |
See More
| Suggests | knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | ccmap |
| Links To Me | |
| Build Report | 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 |
| 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 3.9 | Source Archive |