Pre-requisites

• Clone this repository

  git clone https://github.com/whitehead/humanrnamap
  cd humanrnamap

• Download our dataset and move the files into data/ https://zenodo.org/records/15261543

  unzip mutational_profiles.zip
  mv mutational_profiles/chrom data/chrom
  unzip hg38_fasta.zip
  mv fasta data/fasta
  mv genename.bed data/genename.bed

• Python 3.11 or higher

• VARNA https://varna.lisn.upsaclay.fr/

  wget https://varna.lisn.upsaclay.fr/bin/VARNAv3-93.jar
  mv VARNAv3-93.jar bin/.

• RNAstructure - efn2, Fold, ct2dot https://rna.urmc.rochester.edu/RNAstructureDownload.html efn2: Version 6.4 (December 8, 2021). Mathews Lab, University of Rochester.

  wget https://rna.urmc.rochester.edu/Releases/current/RNAstructureLinuxTextInterfaces64bit.tgz
  tar xvfz RNAstructureLinuxTextInterfaces64bit.tgz
  cd RNAstructure
  make Fold
  make efn2
  make ct2dot
  cp exe/Fold ../bin/.
  cp exe/efn2 ../bin/.
  cp exe/ct2dot ../bin/.
  cp -r data_tables ../bin/.

Installation

Virtual Environment & Dependencies

1. Create a virtual environment:

   python -m venv venv

2. Activate the virtual environment:

   source venv/bin/activate

3. Install the dependencies:

   pip install -r requirements.txt