Software and databases used in Babelomics 4.0

Software

Babelomics 4.0 has been mainly written in Java, but for some of the functionalities we have used R 2.10 and Bioconductor 2.5, and also some external Java libraries:

  • 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.

Databases

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: