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Table 3 Comparing InSilico DB with other databases

From: InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor

InSilico DB functionality Description GEO comparison Expression Atlas
Data sources    
Public repositories Support main platforms of GEO, SRA and notable public datasets All platforms supported, limited to submissions Support for Array-Express
Grouping New datasets created by subsetting and combining datasets   
Biocuration    
Collaborative Commonalizing biocuration effort through collaborative platform   
Vocabulary User-defined tabular structured text Free text Ontologies & free text
Versioning Multiple, user-contributed, batch submissions from biocuration projects, and in-house biocurator In-house biocuration In-house biocuration
Augment Enrich curation with analysis results   
Data management    
  Processing raw data with latest algorithms, for example, fRMA for microarrays, TopHat+Cufflinks for RNA-Seq   
  Datasets can be shared at progressive levels, including groups, and published to the InSilico DB public repository   
Data export    
Raw data Raw data are available for download Raw data are available for download Through ArrayExpress links
Output Format Multiple ready-to-use analysis-tool-compatible format (GenePattern, R/Bioconductor and IGV compatible) GEO-defined SOFT and text formats  
Programmatic access InSilico Db R/Bioconductor package Through third-party GEOquery R/Bioconductor package  
  1. SRA, Short Read Archive.