# Isoespy

**isoespy** is an analysis toolkit designed to visualize functional features of transcript isoforms and to illustrate isoform-level expression changes between case and control groups.

## Overview

The tool can be used in two ways:

1.  **Visualization Mode**: Users provide a transcriptome with preexisting annotations (GTF file) and use isoespy solely for visualization—displaying functional features of annotated transcripts and the results of differential expression or usage analyses.
2.  **Analysis Workflow**: Users begin with raw expression data and an unannotated transcriptome. In this workflow, a series of isoespy commands can be executed to predict functional features for each transcript, perform isoform-level differential analyses, and subsequently visualize the results.

In both usage modes, the overarching purpose of isoespy is to enable intuitive understanding of biological differences among transcript isoforms—such as functional distinctions or expression changes between two conditions—through comprehensive and visually interpretable representations.


## Installation

You can install `isoespy` via pip (or from source):

```bash
pip install isoespy
```


## Documentation

For detailed instructions, usage examples, and command references, please refer to the **User Guide**:

- **[User Guide (PDF)](https://drive.google.com/file/d/17T6s2EgrxuKnh7QulpJRDndf-l0yRmCQ/view?usp=share_link)**


## Sample data

Download the example dataset used in the User Guide from the link below.

- **[Sample dataset](https://drive.google.com/drive/folders/15maiG46L-ET5IeerAih_cgJV50FxQ42_?usp=sharing)**


## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

Copyright (c) 2025 Ko Ikemoto
