ABAEnrichment: Gene expression enrichment in human brain regions

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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.

Author
Steffi Grote
Date of publication
None
Maintainer
Steffi Grote <steffi_grote@eva.mpg.de>
License
GPL (>= 2)
Version
1.4.0

View on Bioconductor

Man pages

aba_enrich
Test genes for expression enrichment in human brain regions
ABAEnrichment-package
Gene expression enrichment in human brain regions
get_expression
Get expression data for given genes and brain structure ids
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

Files in this package

ABAEnrichment/DESCRIPTION
ABAEnrichment/NAMESPACE
ABAEnrichment/R
ABAEnrichment/R/RcppExports.R
ABAEnrichment/R/aba_enrich.R
ABAEnrichment/R/detect_identifier.R
ABAEnrichment/R/get_expression.R
ABAEnrichment/R/get_genes_from_regions.R
ABAEnrichment/R/get_name.R
ABAEnrichment/R/get_sampled_substructures.R
ABAEnrichment/R/get_superstructures.R
ABAEnrichment/R/load_by_name.R
ABAEnrichment/R/plot_expression.R
ABAEnrichment/R/rearrange_output.R
ABAEnrichment/R/sysdata.rda
ABAEnrichment/build
ABAEnrichment/build/vignette.rds
ABAEnrichment/inst
ABAEnrichment/inst/CITATION
ABAEnrichment/inst/NEWS
ABAEnrichment/inst/doc
ABAEnrichment/inst/doc/ABAEnrichment.R
ABAEnrichment/inst/doc/ABAEnrichment.Rmd
ABAEnrichment/inst/doc/ABAEnrichment.html
ABAEnrichment/man
ABAEnrichment/man/ABAEnrichment-package.Rd
ABAEnrichment/man/aba_enrich.Rd
ABAEnrichment/man/get_expression.Rd
ABAEnrichment/man/get_name.Rd
ABAEnrichment/man/get_sampled_substructures.Rd
ABAEnrichment/man/get_superstructures.Rd
ABAEnrichment/man/plot_expression.Rd
ABAEnrichment/src
ABAEnrichment/src/RcppExports.cpp
ABAEnrichment/src/blocks.cpp
ABAEnrichment/src/blocks.h
ABAEnrichment/src/gene.cc
ABAEnrichment/src/gene.h
ABAEnrichment/src/genes.cc
ABAEnrichment/src/genes.h
ABAEnrichment/src/go.cc
ABAEnrichment/src/go.h
ABAEnrichment/src/go_graph.cc
ABAEnrichment/src/go_graph.h
ABAEnrichment/src/go_graph_hyper.cc
ABAEnrichment/src/go_graph_hyper.h
ABAEnrichment/src/go_groups.cc
ABAEnrichment/src/go_groups.h
ABAEnrichment/src/go_groups_hyper.cc
ABAEnrichment/src/go_groups_hyper.h
ABAEnrichment/src/go_obj.cc
ABAEnrichment/src/go_obj.h
ABAEnrichment/src/go_obj_hyper.cc
ABAEnrichment/src/go_obj_hyper.h
ABAEnrichment/src/hyper_categorytest.cc
ABAEnrichment/src/hyper_randset.cc
ABAEnrichment/src/idmap.cc
ABAEnrichment/src/idmap.h
ABAEnrichment/src/overall_sign.cc
ABAEnrichment/src/overall_sign.h
ABAEnrichment/src/ran_genelen.cpp
ABAEnrichment/src/ran_genelen.h
ABAEnrichment/src/read_bed.cpp
ABAEnrichment/src/read_bed.h
ABAEnrichment/src/roll.cpp
ABAEnrichment/src/roll.h
ABAEnrichment/src/structures.h
ABAEnrichment/src/transitions.cc
ABAEnrichment/src/transitions.h
ABAEnrichment/src/unlock_environment.cc
ABAEnrichment/src/wilcox_categorytest.cc
ABAEnrichment/src/wilcox_randset.cc
ABAEnrichment/tests
ABAEnrichment/tests/testthat
ABAEnrichment/tests/testthat.R
ABAEnrichment/tests/testthat/test_0load_by_name.R
ABAEnrichment/tests/testthat/test_1get_expression.R
ABAEnrichment/tests/testthat/test_1plot_expression.R
ABAEnrichment/tests/testthat/test_aba_enrich.R
ABAEnrichment/tests/testthat/test_detect_identifier.R
ABAEnrichment/tests/testthat/test_get_name.R
ABAEnrichment/tests/testthat/test_get_sampled_substructures.R
ABAEnrichment/tests/testthat/test_get_superstructures.R
ABAEnrichment/vignettes
ABAEnrichment/vignettes/ABAEnrichment.Rmd
ABAEnrichment/vignettes/Skizze_Fig1.png
ABAEnrichment/vignettes/Skizze_Fig2.png