ABAEnrichment: Gene expression enrichment in human brain regions

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ABAEnrichment")
AuthorSteffi Grote
Bioconductor views GeneExpression GeneSetEnrichment
Date of publicationNone
MaintainerSteffi Grote <steffi_grote@eva.mpg.de>
LicenseGPL (>= 2)
Version1.4.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/RcppExports.R R/aba_enrich.R R/detect_identifier.R R/get_expression.R R/get_genes_from_regions.R R/get_name.R R/get_sampled_substructures.R R/get_superstructures.R R/load_by_name.R R/plot_expression.R R/rearrange_output.R
R/sysdata.rda
build
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_expression.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_name.R tests/testthat/test_get_sampled_substructures.R tests/testthat/test_get_superstructures.R
vignettes
vignettes/ABAEnrichment.Rmd
vignettes/Skizze_Fig1.png
vignettes/Skizze_Fig2.png

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