ABAEnrichment
This package is for version 3.9 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: 3.9
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>
citation("ABAEnrichment")):
Installation
To install this package, start R (version "3.6") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ABAEnrichment")| Introduction to ABAEnrichment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Software |
| Version | 1.14.1 |
| 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), GOfuncR(>= 1.1.2), grDevices, stats, graphics, 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_1.14.1.tar.gz |
| Windows Binary | ABAEnrichment_1.14.1.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | ABAEnrichment_1.14.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ABAEnrichment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ABAEnrichment |
| Bioc Package Browser | https://code.bioconductor.org/browse/ABAEnrichment/ |
| Package Short Url | https://bioconductor.org/packages/ABAEnrichment/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |