title: inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO.
abstract: Microarray technology has become an integral part of biomedical research and increasing amounts of datasets become available through public repositories. However, re-use of these datasets is severely hindered by unstructured, missing or incorrect biological samples information; as well as the wide variety of preprocessing methods in use. The inSilicoDb R/Bioconductor package is a command-line front-end to the InSilico DB, a web-based database currently containing 86 104 expert-curated human Affymetrix expression profiles compiled from 1937 GEO repository series. The use of this package builds on the Bioconductor project's focus on reproducibility by enabling a clear workflow in which not only analysis, but also the retrieval of verified data is supported.
authors.affiliation: CoMo, Department of Computer Science, Vrije Universiteit Brussel, Pleinlaan 2, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. jtaminau@vub.ac.be
authors.forename: Jonatan
authors.initials: J
authors.lastname: Taminau
authors.forename: David
authors.initials: D
authors.lastname: Steenhoff
authors.forename: Alain
authors.initials: A
authors.lastname: Coletta
authors.forename: Stijn
authors.initials: S
authors.lastname: Meganck
authors.forename: Cosmin
authors.initials: C
authors.lastname: Lazar
authors.forename: Virginie
authors.initials: V
authors.lastname: de Schaetzen
authors.forename: Robin
authors.initials: R
authors.lastname: Duque
authors.forename: Colin
authors.initials: C
authors.lastname: Molter
authors.forename: Hugues
authors.initials: H
authors.lastname: Bersini
authors.forename: Ann
authors.initials: A
authors.lastname: Nowé
authors.forename: David Y
authors.initials: DY
authors.lastname: Weiss Solís
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software