AltAnalyze3 Documentation

Welcome to the AltAnalyze3 documentation!

AltAnalyze3 is an advanced Python3 workflow for long-read (LR) and short read analysis. Combine results across samples or technologies for supervised and unsupervised splicing/isoform analyses. See tutorials for examples.

Contents:

• Installation Guide
• Quickstart Tutorial
• Long Read Single-Cell Analysis Tutorial
  • Prerequisites
  • Step-by-Step Preprocessing
  • Next Steps
  • Support

Getting Started

To begin using AltAnalyze3, follow the steps in the Installation Guide section. For a brief overview, visit the Quickstart Tutorial guide.

Key Features

• Integrated long-read isoform analysis.

• Protein-level impacts of splicing and isoforms.

• Automated single-cell and differential analyses.

• Integration of bulk and single-cell data.

• Alternative promoter, retained intron and alternative polyadenylation regulation.

API Documentation

For detailed descriptions of the available modules and their usage, see the api_reference.

Tutorials

Our tutorials cover essential workflows, including:

• Long Read Analysis: Long Read Single-Cell Analysis Tutorial

• Short Read Analysis: tutorials/short_read_analysis

• Differential Analysis: tutorials/differentials

• Splice-ICGS Analysis: tutorials/splice_icgs

Support

If you encounter issues or need assistance, please visit our GitHub repository: https://github.com/SalomonisLab/altanalyze3