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InSiIicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO This publication appears in: Bioinformatics Authors: J. Taminau, D. Frederik Steenhoff, A. Coletta, S. Meganck, V. Cosmin Lazar, V. De Schaetzen Van Brienen, R. Duqué, C. Molter, H. Bersini, A. Nowé and D. Y. Weiss-Solis Volume: 22 Issue: 27 Pages: 3204-3205 Publication Year: 2011
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 RBioconductor 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 1,937 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.
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