ABAEnrichment

DOI: 10.18129/B9.bioc.ABAEnrichment    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ABAEnrichment.

Gene expression enrichment in human brain regions

Bioconductor version: 3.15

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, and besides the standard candidate vs. background gene set enrichment, also three additional tests are implemented, e.g. for cases when genes are ranked instead of divided into candidate and background.

Author: Steffi Grote

Maintainer: Steffi Grote <steffi_grote at eva.mpg.de>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ABAEnrichment")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	GeneExpression, GeneSetEnrichment, Software
Version	1.26.0
In Bioconductor since	BioC 3.2 (R-3.2) (7 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), GOfuncR(>= 1.1.2), grDevices, stats, graphics, utils
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, testthat
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/ABAEnrichment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ABAEnrichment
Package Short Url	https://bioconductor.org/packages/ABAEnrichment/
Package Downloads Report	Download Stats