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title: "reg2gene" author: Inga Patarcic, Altuna Akalin output: github_document

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reg2gene project

https://github.com/BIMSBbioinfo/reg2gene

This repo contains the code for predicting the target genes for regulatory elements

It contains the following:

• regulatory activity quantification per pre-defined region:

  • the code used to quantify enhancer activties across different markers and studies: regActivity()
  • the code used to quantify gene expression across different studies: bwToGeneExp()
  • the code used to match enhancers to potential target genes within pre-defined window around gene TSSes: regActivityAroundTSS()

• enhancer target prediction (targetPrediction)

  • the code for target prediction methods: associateReg2Gene()

• benchmark predicted interactions:

  • the code for benchmarking predicted interactions given some benchmark dataset: benchmarkGI()

• performance metrics (performance):

  • the code for performance metrics via calculating and reporting confusion matrix for tested benchmarked dataset: confusionMatrix() + filterPreBenchGI()

  package installation

    library(devtools)
    install_github("BIMSBbioinfo/reg2gene")