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Code for the Kipoi manuscript
Jupyter Notebook Python Other
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m_kipoi
models/Divergent421
slurm
src
.gitattributes
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Makefile
README.md
env.yaml
setup.cfg
setup.py

README.md

manuscript_code

Code accompanying the Kipoi manuscript

Installation

  1. Install miniconda or anaconda.
  2. Install git-lfs: conda install -c conda-forge git-lfs && git lfs install
  3. Clone this repository: git clone https://github.com/kipoi/manuscript.git && cd manuscript
  4. Run: git lfs pull '-I data/**'
  5. Run: conda env create -f env.yaml. This will install a new conda environment kipoi-manuscript
  6. Activate the environment: source activate kipoi-manuscript
  7. Install the m_kipoi python package for this repository : pip install -e .

Folder organization

  • m_kipoi - python package (contains python functions/classes common across multiple notebooks)
  • src - scripts for running the experiments and producing the figures
    • tf-binding - Figure 2
    • transfer_learnining - Figure 3
    • mutationmaps - Figure 4
    • splicing - Figure 5
  • data - data files
  • models/Divergent421 - (optional) Pre-trained DNA accessibility model (Kipoi format)
  • slurm - (optional) SLURM profile for snakemake https://github.com/Snakemake-Profiles/slurm

Overview by use-cases

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