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.

AuthorSteffi Grote
Date of publicationNone
MaintainerSteffi Grote <steffi_grote@eva.mpg.de>
LicenseGPL (>= 2)
Version1.4.0

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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