- Home
- Bioconductor 3.2
- Software Packages
- ABAEnrichment
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ABAEnrichment")
In most cases, you don't need to download the package archive at all.
ABAEnrichment
|
Gene expression enrichment in human brain regions
Bioconductor version: 3.2
The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function 'aba_enrich' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses. Additional functions provided in this package like 'get_expression' and 'plot_expression' facilitate exploring the expression data.
Author: Steffi Grote
Maintainer: Steffi Grote <steffi_grote at eva.mpg.de>
Citation (from within R,
enter citation("ABAEnrichment")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ABAEnrichment")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ABAEnrichment")
| HTML | ABAEnrichment: gene expression enrichment in human brain regions | |
| Reference Manual |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Software |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.2 (R-3.2) (0.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.2) |
| Imports | Rcpp (>= 0.11.5), gplots (>= 2.14.2), ABAData(>= 0.99.2) |
| LinkingTo | Rcpp |
| Suggests | BiocStyle, knitr, testthat |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ABAEnrichment_1.2.2.tar.gz |
| Windows Binary | ABAEnrichment_1.2.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ABAEnrichment_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | ABAEnrichment_1.2.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ABAEnrichment/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/ABAEnrichment/ |
| 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
