# isoespy: an integrated long-read transcriptome workflow for isoform resolution and visualization

## TL;DR

Isoespy is a new tool that helps scientists analyze and visualize complex RNA data to better understand different gene isoforms and their functions.

## Contribution

Isoespy introduces an integrated workflow for isoform-level analysis and visualization from long-read RNA-seq data.

## Key findings

- Isoespy combines isoform structures, differential expression, and functional annotations in a single pipeline.
- Application to hepatocellular carcinoma data revealed differences in isoform usage and predicted protein functions.

## Abstract

Long-read RNA-seq uncovers complex transcriptome diversity, opening new avenues for isoform-level expression analysis. Nevertheless, the functional diversity of individual isoforms is still poorly understood. We introduce isoespy, an analysis pipeline for integrating isoform structures, differential expression, and functional annotations from long-read RNA-seq data. The workflow integrates third-party open reading frame predictors, juxtaposes isoform expression levels with gene models, and visualizes positional and non-positional user-provided features. We applied isoespy to a transcriptome dataset of hepatocellular carcinoma, identifying differences in isoform usage and predicted protein function. isoespy facilitates the interpretation of transcriptomic complexity through integrated structural and functional visualization.

Isoespy is freely available at https://github.com/kolikem/isoespy.