alice-szeliga/keles-pipeline: A Model to Predict Regulatory and Expression Modulating eQTLs

This model aims to predict regulatory and expression modulating sequences from a set of eQTLs (SNPs, small insertions or deletions). This package takes in mPRA data and outputs scores of predicted regulatory effect. For each eQTL, we look at PWM scores from ENCODE, JASPAR, and FACTORBOOK, as well as Uniprobe k-mer scores, DeepBind model scores, and GM12878-specific ENCODE annotations. This package incorporates code that was originally developed for the CAGI 2015 eQTL causal SNPs challenge, in which the Keles lab ranked 2nd.

install.packages("remotes")
remotes::install_github("alice-szeliga/keles-pipeline")