Swan: a library for the analysis and visualization of long-read transcriptomes
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Abstract
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.
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Subtle differences in the transcription start site between hub isoforms in modules RGL-M6 and RGL-M9 were found.
“we found subtle differences in the TSS between hub isoforms in modules RGL-M6 and RGL-M9 that we show as a splicing summary graph38 (Figure 4I), supporting functional changes mediated by small isoform differences.”
From hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023) · cites this paper as [38]
The subtle transcription start site differences between hub isoforms in modules RGL-M6 and RGL-M9 support functional changes mediated by small isoform differences.
“we found subtle differences in the TSS between hub isoforms in modules RGL-M6 and RGL-M9 that we show as a splicing summary graph38 (Figure 4I), supporting functional changes mediated by small isoform differences.”
From hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023) · cites this paper as [38]
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A survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794 · see citing works
Self-citationAnnotation-free quantification of RNA splicing using LeafCutter
Li, Y. I., Knowles, D. A., Humphrey, J., Barbeira, A. N., Dickinson, S. P., Im, H. K., & Pritchard, J. K. (2018) · Nature Genetics · doi:10.1038/s41588-017-0004-9 · Cited by 765 · see citing works
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Research works printed but not linked: 4
- Harrow J. et al (2012) GENCODE: the reference human genome annotation for the ENCODE project. Genome Res., 22, 1760– 1774. 22955987 PMC3431492
- Katz Y. et al (2015) Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics, 31, 2400– 2402. 25617416 PMC4542614
- Wolf F.A. et al (2018) SCANPY: large-scale single-cell gene expression data analysis. Genome Biol., 19, 15. 29409532 PMC5802054
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hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data
Morabito, S., Reese, F., Rahimzadeh, N., Miyoshi, E., & Swarup, V. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100498 · Cited by 773 · see citing works
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- Authors
- Reese, F., & Mortazavi, A.
- Affiliations
- University of California, Irvine (US)
- Corresponding author
- Mortazavi, Ali
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-11-23
- Volume
- 37
- Issue
- 9
- Pages
- 1322-1323
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC8189675
- OpenAlex
- W3090796778
- Cited by
- 29
- References
- 2
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 7 · 2023: 5 · 2022: 4 · 2021: 2
- FWCI
- 0.89
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
- Funders
- NIH (UM1 HG009443)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- mRNA isoforms, differentially expressed transcripts, exon skipping, intron retention, alternative splicing, PacBio, Oxford Nanopore, HepG2 cells, Python library
- MeSH terms
- Animals, Software, Gene Library, Sequence Analysis, RNA, Anseriformes, Transcriptome
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