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

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see 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
PDF   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

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