ABAEnrichment: Gene Expression Enrichment in Human Brain Regions

ABAEnrichment is an R-package designed to test user-defined genes for expression enrichment in different human brain regions. The package integrates the expression of the input gene set and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. The statistical analysis is performed by the core function aba_enrich which interfaces with the ontology enrichment software FUNC. Additional functions provided in this package are get_expression, plot_expression, get_name, get_id, get_sampled_substructures, get_superstructures and get_annotated_genes supporting the exploration and visualization of the expression data.

Installation

A stable release version can be obtained from Bioconductor.

• Installation from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("ABAEnrichment")

The developmental (this) version can be obtained from the 'devel' version of Bioconductor or directly from GitHub:

• Installation from GitHub

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("sgrote/ABAEnrichment")

Usage

See the package's vignette for a tutorial.
Also refer to the man-pages for single functions, e.g.

library(ABAEnrichment)
?aba_enrich
?get_expression