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

Jonatan Taminau; David Steenhoff; Alain Coletta; Stijn Meganck; Vasile Cosmin Lazar; Virginie De Schaetzen Van Brienen; Robin Duqué; Colin Molter; Hugues Bersini; Ann Nowe; David Y. Weiss-Solis

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

Jonatan Taminau, David Steenhoff, Alain Coletta, Stijn Meganck, Vasile Cosmin Lazar, Virginie De Schaetzen Van Brienen, Robin Duqué, Colin Molter, Hugues Bersini, Ann Nowe, David Y. Weiss-Solis

Computational Modelling

Research output: Contribution to journal › Article

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.

Original language	English
Pages (from-to)	3204-3205
Number of pages	2
Journal	Bioinformatics
Volume	22
Issue number	27
Publication status	Published - 2011

Keywords

microarray data

Cite this

Taminau, Jonatan ; Steenhoff, David ; Coletta, Alain ; Meganck, Stijn ; Lazar, Vasile Cosmin ; De Schaetzen Van Brienen, Virginie ; Duqué, Robin ; Molter, Colin ; Bersini, Hugues ; Nowe, Ann ; Weiss-Solis, David Y. / InSiIicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO. In: Bioinformatics. 2011 ; Vol. 22, No. 27. pp. 3204-3205.

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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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author = "Jonatan Taminau and David Steenhoff and Alain Coletta and Stijn Meganck and Lazar, {Vasile Cosmin} and {De Schaetzen Van Brienen}, Virginie and Robin Duqu{\'e} and Colin Molter and Hugues Bersini and Ann Nowe and Weiss-Solis, {David Y.}",

year = "2011",

language = "English",

volume = "22",

pages = "3204--3205",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "27",

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InSiIicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO. / Taminau, Jonatan; Steenhoff, David; Coletta, Alain; Meganck, Stijn; Lazar, Vasile Cosmin; De Schaetzen Van Brienen, Virginie; Duqué, Robin; Molter, Colin; Bersini, Hugues; Nowe, Ann; Weiss-Solis, David Y.

In: Bioinformatics, Vol. 22, No. 27, 2011, p. 3204-3205.

Research output: Contribution to journal › Article

TY - JOUR

T1 - InSiIicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO

AU - Taminau, Jonatan

AU - Steenhoff, David

AU - Coletta, Alain

AU - Meganck, Stijn

AU - Lazar, Vasile Cosmin

AU - De Schaetzen Van Brienen, Virginie

AU - Duqué, Robin

AU - Molter, Colin

AU - Bersini, Hugues

AU - Nowe, Ann

AU - Weiss-Solis, David Y.

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

KW - microarray data

M3 - Article

VL - 22

SP - 3204

EP - 3205

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 27

ER -

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

Abstract

Keywords

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Cite this