Software and databases used in Babelomics 4.0¶
- For Affymetrix Microarray normalization APT 1.12 and Affy 1.24 packages are used. For the rest of microarrays data normalization we have used some homemade scripts build using Limma 3.2.1 and Biobase 2.6.0
- Limma 3.2.1 and Apache Commons Math 2.1 are used for differential expression and correlation analysis.
- For time/dosage analysis we have used: maSigPro, EMV and Limma 3.2.1.
- Weka 3.7 library has been used for some predictors and clustering analysis.
- For Genomics analysis like Association or Stratification we have used Plink v1.07.
For many of the analysis a cross reference database and a regulatory and pathway information is needed, here you can find which genomics and functional databases we have integrated to build Babelomics 4.0 and Babelomics 4.1:
- Ensembl 56 and Biomart are used as a main biological database, many of the Xref IDs and SNPs inforamtion are extracted from theses databases.
- Gene Ontology used to build theses releases is from December of 2009.
- For regulatory info we have integrated: ORegAnno Aug 2009 and calculated TFSB using Jaspar 2009 database.
- Kegg 52.1, Reactome 31 and Biocarta are used for pathway extraction.
- For miRNA information and targets miRBase 14 has been used.