Data analysis results for: "MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions"

This release contains the data produced by code hosted on github.com/paulsengroup/2021-modle-paper-001-data-analysis and archived on Zenodo (10.5281/zenodo.6425490).
This data and the code used to generate it is published in support of the following preprint:
MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions (https://doi.org/10.1101/2022.04.13.488157).

Each archive contains the output data produced by one of the workflows hosted on github.com/paulsengroup/2021-modle-paper-001-data-analysis.

Furthermore, archives contain README files describing the archive layout and content.

What follows is a brief description of the archives part of this upload:

• 2021-modle-paper-001-data-containers.tar.zst: archive of the containers used as part of the data analysis. Images are hosted on DockerHub and GHCR.io and are automatically downloaded by the workflows. This archive just serves as a backup in the remote possibility that the original images become unavailable.
• 2021-modle-paper-001-data-downloads.tar.zst: archive containing input files used by workflows for data analysis. Files are automatically downloaded by workflows when appropriate. This is archive is also a backup in case the files become unavailable. File URLs are available here, while file checksums can be found here.
• 2021-modle-paper-001-data-input.tar.zst: this archive contains the files produced by the fetch_data.nf workflow.
• 2021-modle-paper-001-data-output-benchmarks.tar.zst: archive containing the results of the performance benchmark. These files were produced by workflow run_benchmarks.nf.
• 2021-modle-paper-001-data-output-heatmap-comparison.tar.zst: archive containing the output of workflow make_heatmaps_comparison.nf.
• 2021-modle-paper-001-data-output-optimize-modle-sim-params.tar.zst: archive containing the output of the extrusion barrier parameter optimization carried out by workflow optimize_modle_sim_params.nf.
• 2021-modle-paper-001-data-output-preprocessing.tar.zst: archive containing the preprocessed input files. Preprocessing is carried out by workflow preprocess_data.nf.