H2M Documentation

H2M is a python package for precise modeling of human vairants in the mouse genome.

H2M’s main functions are:

1. Querying mouse orthologous genes with human genes input.

2. Generating homologous mouse mutations with a list of input human mutations. The input format is extremely flexible, allowing for users to input a list of genome coordinates or sequences with desired edits.

Package Installation

H2M is available through the python package index. To install, use pip:

pip install h2m

Contents:

• Quick Start
  • Installation
  • Importing packages
  • Loading data
  • Query mouse orthologous genes
  • Get transcript ID (Internet connection needed)
  • Modeling human variants in the mouse genome
    • Input
    • Usage
    • Alternative modeling
    • Original modeling with uncertain effects
    • Additional function 1: modeling for base editing
    • Additional function 2: modeling by amino acid change input
  • Batch Processing
    • Input format
      • Read from cBioPortal
      • Read from ClinVar
      • Read from GenomAD
    • Get canonical transcript ID of human genes if needed, no internet connection needed
    • Get canonical transcript ID of mouse genes, no internet connection needed
    • Batch modeling
    • Result visualization
• Jupyter Notebook Tutorial
• Complete Function Documentation
  • genome_loader()
  • anno_loader()
  • cbio_reader()
  • clinvar_reader()
  • genomad_reader()
  • get_tx_id()
  • get_tx_batch()
  • query()
  • query_batch()
  • model()
  • model_batch()
  • visualization()
• Downstream Genome Editing Librabry Design Tool
  • PEGG: Prime Editing Guide Generator
• About H2M