inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO. 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. Availability: inSilicoDb is available as part of the Bioconductor project. There is a companion web interface that can be used for browsing available datasets before importing them into R/Bioconductor (http://insilico.ulb.ac.be).
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References in zbMATH (referenced in 2 articles )
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- von Stechow, Louise (ed.); Delgado, Alberto Santos (ed.): Computational cell biology. Methods and protocols (2018)
- Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)