README.md

In BIMSBbioinfo/reg2gene: Predicting the target genes for regulatory elements

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

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")
  

BIMSBbioinfo/reg2gene documentation built on May 3, 2019, 6:42 p.m.