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| Method name | Reference | Brief description | Computer platform | Web interface | Availability | URL |
|
| Babelomics | Al-Shahrour et al. 2006 | Web-based tools for genomic data analysis. Gene annotations include predicted microRNA | Any platform, web browser | yes | Free access | http://www.babelomics.org/ |
| M@ia | Le Bechec et al. 2008 | Modular tools for genomic data analysis. Gene annotations include predicted microRNA | Linux, MacOs, Windows. PHP language, Apache web server and MySQL database required | no | Open-source | http://maia.genouest.org/ |
| TIGR Multiexperiment Viewer (MeV) | | Integrated environment for -omics data analysis. Gene annotations include predicted microRNA | Windows, MacOs; Java required. | no | Free executable | http://www.tm4.org/mev.html |
| BRB-ArrayTools | | Tools for -omics data analysis. The working environment is Microsoft Excel, an R engine is providing to Excel through and add-in module. Gene annotations include predicted microRNA | Windows. Java, Excel and R language required | no | Free executable | http://linus.nci.nih.gov/~brb/download.html |
| GeneSpring GX | | Integrated environment for -omics data analysis. Gene annotations include predicted microRNA | Windows, Java required | no | Commercial from Agilent Technologies, free trial | http://www.silicongenetics.com/ |
| Ingenuity Pathway Analysis | | Integrated environment for -omics data analysis. Gene annotations include predicted microRNA. Functional annotation and analysis of biological networks. | Windows, Java required | no | Commercial from Ingenuity Systems Inc., free trial | http://www.ingenuity.com/index.html |
| R Bionconductor | | A common open source environment for -omics data analysis and statistics. It includes tools for microRNA analysis and annotation. | Linux, MacOs, Windows. | no | Open Source | http://www.bioconductor.org/ |
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