inSilicoDb statistics

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inSilicoDb specifications

Information


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
Requirements
Biobase, R(>=2.11.0), RCurl, rjson
Maintained Yes

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  • person_outline inSilicoDb Team <>

Publications for inSilicoDb

inSilicoDb in publications

 (15)
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, http://www.ncbi.nlm.nih.gov/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 (https://insilicodb.com/), and analyzed by using the gsea v2.07 software (http://www.broad.mit.edu/gsea), 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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