To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ABAEnrichment")

In most cases, you don't need to download the package archive at all.

ABAEnrichment

DOI: 10.18129/B9.bioc.ABAEnrichment    

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

Gene expression enrichment in human brain regions

Bioconductor version: Development (3.7)

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. From version 1.3.5 onwards genomic regions can be provided as input, too; and from version 1.5.9 onwards the function 'get_annotated_genes' offers an easy way to obtain annotations of genes to enriched or user-defined brain regions.

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("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ABAEnrichment")

Documentation

HTML R Script Introduction to ABAEnrichment
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, GeneSetEnrichment, Software
Version 1.9.0
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License GPL (>= 2)
Depends R (>= 3.4)
Imports Rcpp (>= 0.11.5), gplots (>= 2.14.2), gtools (>= 3.5.0), ABAData(>= 0.99.2), data.table (>= 1.10.4), grDevices, stats, utils
LinkingTo Rcpp
Suggests BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me ABAData
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ABAEnrichment_1.9.0.tar.gz
Windows Binary ABAEnrichment_1.9.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) ABAEnrichment_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ABAEnrichment
Package Short Url http://bioconductor.org/packages/ABAEnrichment/
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