ABAEnrichment
This package is for version 3.6 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: 3.6
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("ABAEnrichment")):
Installation
To install this package, start R (version "3.4") 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
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 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), grDevices, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, testthat |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | ABAData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ABAEnrichment_1.8.0.tar.gz |
| Windows Binary | ABAEnrichment_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | ABAEnrichment_1.8.0.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 | https://bioconductor.org/packages/ABAEnrichment/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |