DOI: 10.18129/B9.bioc.ABAEnrichment    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ABAEnrichment.

Gene expression enrichment in human brain regions

Bioconductor version: 3.10

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>

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biocViews GeneExpression, GeneSetEnrichment, Software
Version 1.16.0
In Bioconductor since BioC 3.2 (R-3.2) (4.5 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, graphics, utils
LinkingTo Rcpp
Suggests BiocStyle, knitr, testthat
Depends On Me
Imports Me
Suggests Me ABAData
Links To Me
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Source Package ABAEnrichment_1.16.0.tar.gz
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