inSilicoDb statistics

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inSilicoDb specifications


Unique identifier OMICS_12549
Name inSilicoDb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.0
Stability Stable
Biobase, R(>=2.11.0), RCurl, rjson
Maintained Yes


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Publications for inSilicoDb

inSilicoDb in publications

PMCID: 5700969
PMID: 29170406
DOI: 10.1038/s41467-017-01430-6

[…] transcriptional profiles and clinical annotations were downloaded from the national center for biotechnology information gene expression omnibus (geo, via the insilicodb package in r/bioconductor. in order to minimize undesired variations from different platforms, only samples probed with affymetrix human genome u133 plus 2.0 (hg-u133_plus_2) array […]

PMCID: 5565741
PMID: 28855977
DOI: 10.1016/j.csbj.2017.07.005

[…] the first step towards integrating different kinds of information in a model is to collect the raw data required to build the information. for example, in the context of the physiome project, the insilicodb collects physiological experimental data (time-series and image-based morphological models)¬†. information in the database can be used together with modules representing biological […]

PMCID: 5384279
PMID: 28387221
DOI: 10.1038/srep45828

[…] gse31519, gse3494, gse42568, gse45255, gse4922, gse5327, gse6532, gse7390 and gse9195) were obtained on the affymetrix u133a or u133 plus 2.0 expression array. these samples were collected from insilicodb database and normalized using frma method. a final combined dataset compiling 4,801 breast tumor samples was generated using insilicomerging r package and combat algorithm, an empirical […]

PMCID: 5428028
PMID: 28298645
DOI: 10.1038/s41598-017-00269-7

[…] tumors, and gsea was used to evaluate gene sets enriched for either negatively or positively correlated genes. published gse20238 was downloaded from the insilico db genomic datasets hub (, and analyzed by using the gsea v2.07 software (, as previously described. to account for gene-gene correlations in the enrichment analysis, gsea p […]

PMCID: 5747381
PMID: 29072056
DOI: 10.22034/APJCP.2017.18.10.2629

[…] via ppi network approach and enrichment analysis of degs to find functional gene sets related to ch-r/ch-s driver genes., gene expression profile of gse25066 including 508 samples downloaded from insilicodb, a genomics data repository. the gse25066 expression profile is based on the gpl96 (affymetrix human genome u133a array) that preprocessed by frma method (mccall et al., 2010)., a linear […]

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inSilicoDb institution(s)
CoMo, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium; IRIDIA-CoDE, Université Libre de Bruxelles, Brussels, Belgium; ETRO, Department of Electronics and Informatics, Vrije Universiteit Brussel, Brussels, Belgium

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