ABAEnrichment

DOI: 10.18129/B9.bioc.ABAEnrichment    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ABAEnrichment.

Gene expression enrichment in human brain regions

Bioconductor version: 3.8

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 "3.5") and enter:

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

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ABAEnrichment")

 

HTML	R Script	Introduction to ABAEnrichment
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneSetEnrichment, Software
Version	1.12.0
In Bioconductor since	BioC 3.2 (R-3.2) (3.5 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, utils
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	ABAData
Links To Me
Build Report

Package Archives

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

Source Package	ABAEnrichment_1.12.0.tar.gz
Windows Binary	ABAEnrichment_1.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	ABAEnrichment_1.12.0.tgz
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	http://bioconductor.org/packages/ABAEnrichment/
Package Downloads Report	Download Stats