Bernardo Aguzzoli Heberle, Madeline L Page, Emil K Gustavsson, Mina Ryten, Mark T W Ebbert
{"title":"RNApysoforms: fast rendering interactive visualization of RNA isoform structure and expression in Python.","authors":"Bernardo Aguzzoli Heberle, Madeline L Page, Emil K Gustavsson, Mina Ryten, Mark T W Ebbert","doi":"10.1093/bioadv/vbaf057","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>Alternative splicing generates multiple RNA isoforms from a single gene, enriching genetic diversity and impacting gene function. Effective visualization of these isoforms and their expression patterns is crucial but challenging due to limitations in existing tools. Traditional genome browsers lack programmability, while other tools offer limited customization, produce static plots, or cannot simultaneously display structures and expression levels. RNApysoforms was developed to address these gaps by providing a Python-based package that enables concurrent visualization of RNA isoform structures and expression data. Leveraging plotly and polars libraries, it offers an interactive, customizable, and faster-rendering framework suitable for web applications, enhancing the analysis and dissemination of RNA isoform research.</p><p><strong>Availability and implementation: </strong>RNApysoforms is a Python package available at (https://github.com/UK-SBCoA-EbbertLab/RNApysoforms) and (https://zenodo.org/records/14941190) via an open-source MIT license. It can be easily installed using the pip package installer for Python. Thorough documentation and usage vignettes are available at: https://rna-pysoforms.readthedocs.io/en/latest/.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"5 1","pages":"vbaf057"},"PeriodicalIF":2.4000,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11964586/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbaf057","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
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Abstract
Summary: Alternative splicing generates multiple RNA isoforms from a single gene, enriching genetic diversity and impacting gene function. Effective visualization of these isoforms and their expression patterns is crucial but challenging due to limitations in existing tools. Traditional genome browsers lack programmability, while other tools offer limited customization, produce static plots, or cannot simultaneously display structures and expression levels. RNApysoforms was developed to address these gaps by providing a Python-based package that enables concurrent visualization of RNA isoform structures and expression data. Leveraging plotly and polars libraries, it offers an interactive, customizable, and faster-rendering framework suitable for web applications, enhancing the analysis and dissemination of RNA isoform research.
Availability and implementation: RNApysoforms is a Python package available at (https://github.com/UK-SBCoA-EbbertLab/RNApysoforms) and (https://zenodo.org/records/14941190) via an open-source MIT license. It can be easily installed using the pip package installer for Python. Thorough documentation and usage vignettes are available at: https://rna-pysoforms.readthedocs.io/en/latest/.
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