swMATH ID: 17288
Software Authors: Taminau J, Steenhoff D, Coletta A et al
Description: 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).
Homepage: http://bioinformatics.oxfordjournals.org/content/27/22/3204.short
Dependencies: R
Related Software: GEOquery; TopHat; KEGG; edgeR; Bioconductor; R; Negatome; MatrixDB; InnateDB; HuPho; miRNet; SQUAD; Jimena; ClueGO; gcrma; RedeR; STRINGdb; ANIMO; PRS; NET-SYNTHESIS
Cited in: 2 Documents

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