Affordable Access

deepdyve-link deepdyve-link
Publisher Website

inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO.

Authors
  • Taminau, Jonatan
  • Steenhoff, David
  • Coletta, Alain
  • Meganck, Stijn
  • Lazar, Cosmin
  • de Schaetzen, Virginie
  • Duque, Robin
  • Molter, Colin
  • Bersini, Hugues
  • Nowé, Ann
  • Weiss Solís, David Y
Type
Published Article
Journal
Bioinformatics (Oxford, England)
Publication Date
Nov 15, 2011
Volume
27
Issue
22
Pages
3204–3205
Identifiers
DOI: 10.1093/bioinformatics/btr529
PMID: 21937664
Source
Medline
License
Unknown

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.

Report this publication

Statistics

Seen <100 times