Welcome to the documentation for ortho_seqs!

Introduction:

This documentation accompanies the ortho_seqs python command line tool that computes multivariate tensor-based orthogonal polynomials based on DNA, RNA or protein sequence data and maps corresponding phenotypic information onto the sequence space.

Guide

• Background & Quickstart
  • ortho_seqs
  • Documentation
  • Usage
    • First, install an environment with dependencies for this package:
    • Then, install the package:
    • Gather the input file(s) needed.
    • Then, to run the commandline tool:
    • Flags & Functionality
  • Results & Outputs
    • Generating logo plot
    • Running ortho_seqs
  • The rf1d class
  • To run the GUI
  • Support
  • Roadmap
  • Contribution
  • Authors and acknowledgements
  • License
• Tutorial: Running a sample dataset (protein sequences)
  • 1. Setting Up Your Computer to Run ortho_seqs
  • 2. Your dataset
  • 3. Executing Ortho_Seqs
  • 4. Obtained Outputs
    • CLI Outputs
    • Histogram and Spreadsheet of Covariances
    • rFon1D Graph
  • 4. The rf1d Class
• Tutorial: Visualizing your rFon1D results
  • 1. Requirements for rf1d-viz
  • 2. rf1d-viz flags:
  • 3. Running rf1d-viz
  • Guided example with the Sidhu dataset
• Tutorial: Generating a sequence logo plot
  • 1. Requirements for logo-plot
  • 2. logo-plot flags:
  • 3. Running logo-plot:
  • 4. Guided example with test dataset:
• License
• Get Further Help
  • Contact

Indices and tables

• Index

• Module Index

• Search Page