ABAEnrichment: Gene expression enrichment in human brain regions
Version 1.6.0

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.

AuthorSteffi Grote
Bioconductor views GeneExpression GeneSetEnrichment
Date of publicationNone
MaintainerSteffi Grote <steffi_grote@eva.mpg.de>
LicenseGPL (>= 2)
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ABAEnrichment")

Getting started

Package overview

Popular man pages

ABAEnrichment-package: Gene expression enrichment in human brain regions
get_annotated_genes: Get genes that are expressed in enriched or user-defined...
get_expression: Get expression data for given genes and brain structure IDs
get_id: Get the structure ID of a brain region given its name
get_name: Get the full name of a brain region given structure IDs
get_superstructures: Returns all superstructures of a brain region using the Allen...
plot_expression: Plot expression data for given genes and brain structure IDs
See all...

All man pages Function index File listing

Man pages

aba_enrich: Test genes for expression enrichment in human brain regions
ABAEnrichment-package: Gene expression enrichment in human brain regions
get_annotated_genes: Get genes that are expressed in enriched or user-defined...
get_expression: Get expression data for given genes and brain structure IDs
get_id: Get the structure ID of a brain region given its name
get_name: Get the full name of a brain region given structure IDs
get_sampled_substructures: Return sampled substructures of a given brain region
get_superstructures: Returns all superstructures of a brain region using the Allen...
plot_expression: Plot expression data for given genes and brain structure IDs

Functions

ABAEnrichment Man page
ABAEnrichment-package Man page
aba_enrich Man page Source code
detect_identifier Source code
get_annotated_genes Man page Source code
get_expression Man page Source code
get_genes_from_regions Source code
get_id Man page Source code
get_name Man page Source code
get_one_name Source code
get_sampled_substructures Man page Source code
get_signi_combis Source code
get_superstructures Man page Source code
hyper_category_test Source code
hyper_randset Source code
load_by_name Source code
merge_bed Source code
merge_chrom Source code
plot_expression Man page Source code
rearrange_output Source code
to_wide Source code
unlock_environment Source code
wilcox_category_test Source code
wilcox_randset Source code

Files

DESCRIPTION
NAMESPACE
R
R/RcppExports.R
R/aba_enrich.R
R/detect_identifier.R
R/get_annotated_genes.R
R/get_expression.R
R/get_genes_from_regions.R
R/get_id.R
R/get_name.R
R/get_sampled_substructures.R
R/get_superstructures.R
R/load_by_name.R
R/merge_bed.R
R/plot_expression.R
R/rearrange_output.R
R/sysdata.rda
build
build/partial.rdb
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ABAEnrichment.R
inst/doc/ABAEnrichment.Rmd
inst/doc/ABAEnrichment.html
man
man/ABAEnrichment-package.Rd
man/aba_enrich.Rd
man/get_annotated_genes.Rd
man/get_expression.Rd
man/get_id.Rd
man/get_name.Rd
man/get_sampled_substructures.Rd
man/get_superstructures.Rd
man/plot_expression.Rd
src
src/RcppExports.cpp
src/blocks.cpp
src/blocks.h
src/gene.cc
src/gene.h
src/genes.cc
src/genes.h
src/go.cc
src/go.h
src/go_graph.cc
src/go_graph.h
src/go_graph_hyper.cc
src/go_graph_hyper.h
src/go_groups.cc
src/go_groups.h
src/go_groups_hyper.cc
src/go_groups_hyper.h
src/go_obj.cc
src/go_obj.h
src/go_obj_hyper.cc
src/go_obj_hyper.h
src/hyper_categorytest.cc
src/hyper_randset.cc
src/idmap.cc
src/idmap.h
src/overall_sign.cc
src/overall_sign.h
src/ran_genelen.cpp
src/ran_genelen.h
src/read_bed.cpp
src/read_bed.h
src/roll.cpp
src/roll.h
src/structures.h
src/transitions.cc
src/transitions.h
src/unlock_environment.cc
src/wilcox_categorytest.cc
src/wilcox_randset.cc
tests
tests/testthat
tests/testthat.R
tests/testthat/test_0load_by_name.R
tests/testthat/test_1get_expression.R
tests/testthat/test_1plot_expression.R
tests/testthat/test_aba_enrich.R
tests/testthat/test_detect_identifier.R
tests/testthat/test_get_annotated_genes.R
tests/testthat/test_get_id.R
tests/testthat/test_get_name.R
tests/testthat/test_get_sampled_substructures.R
tests/testthat/test_get_superstructures.R
tests/testthat/test_merge_bed.R
vignettes
vignettes/ABAEnrichment.Rmd
vignettes/Skizze_Fig1.png
vignettes/Skizze_Fig2.png
ABAEnrichment documentation built on May 20, 2017, 9:38 p.m.