Codebase for FOCS, a new method for inferring enhancer-promoter (E-P) links and for integrative analysis of E-P links

Additional information about running FOCS can be found here

You can download the database here. The database includes preprocessed RData files of ENCODE, Roadmap Epigenomics, FANTOM5, and GRO-seq:

1. Predicted E-P links
2. Genomic positions of enhancers and promoters
3. Enhancer/promoter count/RPKM profiles
4. Sample annotations

In addition the database includes external data for integrative analysis of E-P links:

1. ChIA-PET interactions mediated by POL2 of 4 cell types (MCF7, HCT-116, K562 and Hela-S3) taken from GSE39495
2. Genomic positions of GTEx eQTL data (V6 and V6p builds) taken from GTEx Portal

Please make sure you have the following pre-installed R packages:

• pscl
• MASS
• parallel
• AUC
• glmnet
• Matching
• RColorBrewer
• GenomicRanges
• ggplot2

Please note that you can run FOCS only under linux platform

First create directories:

1. mkdir focs
2. cd focs
3. mkdir data
4. mkdir scripts
5. mkdir tmp

Copy the scripts in the R folder to ../focs/scripts/ folder

Additional instructions are given within tutorial.R script file