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Swan: a library for the analysis and visualization of long-read transcriptomes
MOTIVATION: Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transc...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189675/ https://www.ncbi.nlm.nih.gov/pubmed/32991665 http://dx.doi.org/10.1093/bioinformatics/btaa836 |
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author | Reese, Fairlie Mortazavi, Ali |
author_facet | Reese, Fairlie Mortazavi, Ali |
author_sort | Reese, Fairlie |
collection | PubMed |
description | MOTIVATION: Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transcript models. RESULTS: Swan finds 4909 differentially expressed transcripts between cell lines HepG2 and HFFc6, including 279 that are differentially expressed even though the parent gene is not. Additionally, Swan discovers 285 reproducible exon skipping and 47 intron retention events not recorded in the GENCODE v29 annotation. AVAILABILITY AND IMPLEMENTATION: The Swan library for Python 3 is available on PyPi at https://pypi.org/project/swan-vis/ and on GitHub at https://github.com/mortazavilab/swan_vis. |
format | Online Article Text |
id | pubmed-8189675 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-81896752021-06-10 Swan: a library for the analysis and visualization of long-read transcriptomes Reese, Fairlie Mortazavi, Ali Bioinformatics Applications Notes MOTIVATION: Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transcript models. RESULTS: Swan finds 4909 differentially expressed transcripts between cell lines HepG2 and HFFc6, including 279 that are differentially expressed even though the parent gene is not. Additionally, Swan discovers 285 reproducible exon skipping and 47 intron retention events not recorded in the GENCODE v29 annotation. AVAILABILITY AND IMPLEMENTATION: The Swan library for Python 3 is available on PyPi at https://pypi.org/project/swan-vis/ and on GitHub at https://github.com/mortazavilab/swan_vis. Oxford University Press 2020-11-23 /pmc/articles/PMC8189675/ /pubmed/32991665 http://dx.doi.org/10.1093/bioinformatics/btaa836 Text en © The Author(s) 2020. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Reese, Fairlie Mortazavi, Ali Swan: a library for the analysis and visualization of long-read transcriptomes |
title | Swan: a library for the analysis and visualization of long-read transcriptomes |
title_full | Swan: a library for the analysis and visualization of long-read transcriptomes |
title_fullStr | Swan: a library for the analysis and visualization of long-read transcriptomes |
title_full_unstemmed | Swan: a library for the analysis and visualization of long-read transcriptomes |
title_short | Swan: a library for the analysis and visualization of long-read transcriptomes |
title_sort | swan: a library for the analysis and visualization of long-read transcriptomes |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189675/ https://www.ncbi.nlm.nih.gov/pubmed/32991665 http://dx.doi.org/10.1093/bioinformatics/btaa836 |
work_keys_str_mv | AT reesefairlie swanalibraryfortheanalysisandvisualizationoflongreadtranscriptomes AT mortazaviali swanalibraryfortheanalysisandvisualizationoflongreadtranscriptomes |