Dataset Information
Isoespy: an integrated long-read transcriptome workflow for isoform resolution and visualization.
Ontology highlight
ABSTRACT: Summary
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.Availability and implementation
Isoespy is freely available at https://github.com/kolikem/isoespy.
SUBMITTER: Ikemoto K
PROVIDER: S-EPMC12935161 | biostudies-literature | 2026
REPOSITORIES: biostudies-literature
Publications
isoespy: an integrated long-read transcriptome workflow for isoform resolution and visualization.
Bioinformatics advances 20260213 1
<h4>Summary</h4>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 m ...[more]
