天鹅：一个用于长读转录组分析和可视化的库。
Swan: a library for the analysis and visualization of long-read transcriptomes.
机构信息
Department of Developmental and Cell Biology.
Center for Complex Biological Systems, UC Irvine, Irvine, CA 92697, USA.
出版信息
Bioinformatics. 2021 Jun 9;37(9):1322-1323. doi: 10.1093/bioinformatics/btaa836.
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.
动机
长读 RNA 测序技术，如 PacBio 和 Oxford Nanopore，已经发现了大量新的转录本异构体，这些异构体使用当前可用的工具进行可视化分析非常困难。我们引入了 Swan Python 库，该库旨在分析和可视化转录本模型。
结果
Swan 在 HepG2 和 HFFc6 细胞系之间发现了 4909 个差异表达的转录本，其中 279 个转录本即使在父基因没有差异表达的情况下也存在差异表达。此外，Swan 发现了 285 个可重复的外显子跳跃和 47 个 GENCODE v29 注释中未记录的内含子保留事件。
可用性和实现
Swan Python 3 库可在 PyPi（https://pypi.org/project/swan-vis/）和 GitHub（https://github.com/mortazavilab/swan_vis）上获取。
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