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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ABAEnrichment")
In most cases, you don't need to download the package archive at all.
ABAEnrichment
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Gene expression enrichment in human brain regions
Bioconductor version: Release (3.5)
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("https://bioconductor.org/biocLite.R")
biocLite("ABAEnrichment")
Documentation
| HTML | R Script | ABAEnrichment: gene expression enrichment in human brain regions |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (2 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.2) |
| Imports | Rcpp (>= 0.11.5), gplots (>= 2.14.2), gtools (>= 3.5.0), ABAData(>= 0.99.2) |
| 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_1.6.0.tar.gz |
| Windows Binary | ABAEnrichment_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | ABAEnrichment_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ABAEnrichment |
| Package Short Url | http://bioconductor.org/packages/ABAEnrichment/ |
| Package Downloads Report | Download Stats |
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