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ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.

ABSTRACT: We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages.

Availability and implementation

ABAEnrichment was implemented as an R package and is available under GPL (≥ 2) from the Bioconductor website (http://bioconductor.org/packages/3.3/bioc/html/ABAEnrichment.html).

Contacts

steffi_grote@eva.mpg.de, kelso@eva.mpg.de or michael_dannemann@eva.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.

SUBMITTER: Grote S

PROVIDER: S-EPMC5048072 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.

Grote Steffi S Prüfer Kay K Kelso Janet J Dannemann Michael M

Bioinformatics (Oxford, England) 20160626 20

We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages.<h4 ...[more]

PMID: 27354695

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