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Welcome to reactIDR wiki!

How to start

git clone https://github.com/carushi/reactIDR
cd reactIDR/
python setup.py  build_ext -b reactIDR/
cd ../example && bash training.sh    # Run test

Requirement

• python3
• numpy
• scikit-learn
• optional
  • seaborn (for visualization)
  • pandas (for visualization)
  • pymc (for pvalue-based score modeling)

What is your input

• Bam file

  • Use docker image to convert it to the bed file
  • Move to tutorial
  • Our shell script is also available here

• Bed file

  • Use our scripts to convert it to the tab file
  • Move to tutorial

• Tab file (as shown below)

  • Run reactIDR!
  • separated by <tab> and ;
  • Move to tutorial

key       <tab> score1          <tab> score2        <tab> (score3)
gene name <tab> 1;2;3;0;4;1;... <tab> 2;5;10;11;... <tab> ()