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Dependancies

  • Python3
    • Numpy
    • Scipy
    • Scikit-Learn
    • Pandas
  • R (>3.3)
  • PEER
  • RPy2

Steps

Code

git clone https://github.com/andrewquitadamo/matrix_eqtl_pipeline.git  
wget https://raw.githubusercontent.com/shilab/meQTL_functions/master/R/mxeqtl.R -P code/  
python3 code/modify_matrix_eqtl.py

Dependancies

apt install python-setuptools  
apt update  
apt install python3-pip  
python3 -m pip install scikit-learn  
python3 -m pip install scipy  
#python3 -m pip install numpy  
python3 -m pip install pandas  

sudo add-apt-repository "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -sc)/"  
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9  
sudo add-apt-repository ppa:marutter/rdev  
sudo apt-get update  
sudo apt-get upgrade  
sudo apt-get install r-base  
wget https://github.com/downloads/PMBio/peer/R_peer_source_1.3.tgz  
tar -xvzf R_peer_source_1.3.tgz  
R CMD INSTALL R_peer_source_1.3.tgz  

python3 -m pip install rpy2