Dalgarno et al. (In preparation)
High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression
Code to create figures can be found in this Jupyter Notebook (analysis_and_figures.ipynb).
Data to create figures can be found on Zenodo ().
To install:
- Clone the github repository, download data from Zenodo.
- Setup the conda environment with: conda env create -f hic_env.yml. Make sure to edit the last line of the yml file accordingly. Activate the environment.
- Install the required versions of cluster profiler in R by running: install.packages(pkgs = "https://www.bioconductor.org/packages/3.17/bioc/src/contrib/clusterProfiler_4.8.3.tar.gz", repos = NULL) install.packages(pkgs = "https://www.bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Hs.eg.db_3.17.0.tar.gz", repos = NULL) install.packages(pkgs = "https://www.bioconductor.org/packages/3.17/data/annotation/src/contrib/GO.db_3.17.0.tar.gz", repos = NULL)
- Set up R to run with jupyter: R -e ‘IRkernel::installspec()’
- Set up bash to run with jupyter: python -m bash_kernel.install