title: "reg2gene" author: Inga Patarcic, Altuna Akalin output: github_document
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()
library(devtools) install_github("BIMSBbioinfo/reg2gene")