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reg2gene.Rproj

README.md


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


reg2gene project

https://github.com/BIMSBbioinfo/reg2gene Build Status codecov.io

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")