PGS: Population-based Genome Structures modeling tools package

PGS is a population-based 3D genome-modeling package implemented in Python. The software takes Hi-C matrix and chromosome regions segmentation or topological associated domains(TADs) information, which then generates an ensemble of structure population. The software also automatically generates analysis reports, such as structure quality based on scoring parameters, plots of radial positions and contact frequency maps from the structures. The whole codes are wrapped in Python, and users can simply execute it one time.

Note

PGS software will run on high performance computing environment (HPC), such as sun grid engine and TORQUE (pbs script), as well as local machine. But, it is highly recommended to run on HPC because of computational resource and running time.

The code is open source, and available on github.

Here is the overview of PGS pipeline:

Contents:

• Quickstart
  • Installation
  • PGS Helper GUI
  • Using the PGS Helper
  • PGS Helper Output
  • RUN PGS
• Expected Results
  • heatmap
  • intraMatrix
  • radialPlot
  • violations
• Tools
• Frequently Asked Questions
• Alberlab API Reference
  • alab
  • alab.files
• Miscellaneous
  • Organization of the .hmat file
  • Organization of the .hms file
  • Organization of the .hss file
  • Activation distance file

• Index