JBrowse Jupyter: a Python']Python interface to JBrowse 2

被引：2

作者：

Martinez, Teresa De Jesus ^{[1
]}

Hershberg, Elliot A. ^{[1
]}

Guo, Emma ^{[1
]}

Stevens, Garrett J. ^{[1
]}

Diesh, Colin ^{[1
]}

Xie, Peter ^{[1
]}

Bridge, Caroline ^{[2
]}

Cain, Scott ^{[2
]}

Haw, Robin ^{[2
]}

Buels, Robert M. ^{[1
]}

Stein, Lincoln D. ^{[2
]}

Holmes, Ian H. ^{[1
]}

机构：

[1] Univ Calif Berkeley, Dept Bioengn, Stanley Hall, Berkeley, CA 94720 USA

[2] Ontario Inst Canc Res, MaRS Ctr, Adapt Oncol, 661 Univ Ave,Su 510, Toronto, ON M5G 0A3, Canada

来源：

BIOINFORMATICS | 2023年 / 39卷 / 01期

基金：

美国国家卫生研究院;

关键词：

GENOME BROWSER;

D O I：

10.1093/bioinformatics/btad032

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization.Results: We have developed a package that provides a Python interface to JBrowse 2's suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google's Colab notebooks, providing reproducible interactive views.

引用

页数：2

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