Source code and support files for metaMIR, an analysis tool for prediction of microRNA interaction with gene clusters written in R.
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README.md

README.md

metaMIR

metaMIR is a framework to predict in human interactions between microRNAs (miRNA) and clusters of genes. The user provides a set of genes to be targeted, and optionally genes not to be targeted. The analysis is performed to identify miRNAs that may simultaneously interact with a number of genes.

The first part of the analysis makes use of individual prediction scores of interaction between one miRNA and one miRNA. These scores are derived from combination of previously established prediction algorithms. Using experimentally-validated interactions for training and testing, a machine learning approach is used to integrate the results of the established algorithm into a new data set. The resulting scores are based on class prediction probabilities; that is, the likelihood that a miRNA targets a target gene.

The individual scores are used in a combinatorial analysis. All combinations of genes (from a minimum cluster size up to inclusion of all genes) are generated and analyzed for miRNAs which will interact with them. The metaMIR algorithm will return miRNA candidates predicted to co-regulate groups of genes.

A webserver version for ad hoc usage is part of the Freiburg RNA tools webserver, hosted on servers of the Bioinformatics Group, Technical Faculty, University of Freiburg, Germany.

Usage and Installation

In order to run metaMIR locally you have to

  • download the source files (R folder content of this github repo or of release file)
  • download the precompiled reference data miRNA_predictions.tar.gz
  • store and decompress both downloads in one directory
  • call one the main scripts (for details see README in R folder)
    • command line : R --file=metaMIR_cl.R --args <ARGUMENTS_SEE_R_SCRIPT>
    • Rstudio : open and run metaMIR_IDE.R