- Home
- Bioconductor 3.5
- Software Packages
- crossmeta
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("crossmeta")
In most cases, you don't need to download the package archive at all.
crossmeta
|
|
|
|
|
Cross Platform Meta-Analysis of Microarray Data
Bioconductor version: Release (3.5)
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 (from within R,
enter citation("crossmeta")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("crossmeta")
Documentation
| HTML | R Script | crossmeta vignette |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Annotation, BatchEffect, DifferentialExpression, GUI, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.3) |
| Imports | affy(>= 1.52.0), affxparser(>= 1.46.0), AnnotationDbi(>= 1.36.2), Biobase(>= 2.34.0), BiocGenerics(>= 0.20.0), BiocInstaller(>= 1.24.0), ccmap, DT (>= 0.2), data.table (>= 1.10.4), doParallel (>= 1.0.10), doRNG (>= 1.6), fdrtool (>= 1.2.15), foreach (>= 1.4.3), 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), pander (>= 0.6.0), plotly (>= 4.5.6), reshape (>= 0.8.6), RColorBrewer (>= 1.1.2), rdrop2 (>= 0.7.0), stringr (>= 1.2.0), sva(>= 3.22.0), shiny (>= 1.0.0), stats (>= 3.3.3) |
| LinkingTo | |
| Suggests | knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | ccmap |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | crossmeta_1.2.0.tar.gz |
| Windows Binary | crossmeta_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | crossmeta_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/crossmeta |
| Package Short Url | http://bioconductor.org/packages/crossmeta/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
