OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies

被引:2
作者
Ernst, Terrence R. [1 ]
Blischak, John D. [1 ]
Nordlund, Paul [1 ]
Dalen, Joe [1 ]
Moore, Justin [1 ,3 ]
Bhamidipati, Akshay [1 ]
Dwivedi, Pankaj [1 ,4 ]
LoGrasso, Joe [1 ]
Curado, Marco Rocha [2 ]
Engelmann, Brett Warren [1 ]
机构
[1] AbbVie Inc, 1 North Waukegan Rd, N Chicago, IL 60064 USA
[2] AbbVie Deutschland GmbH & Co KG, Ludwigshafen, Germany
[3] Baylor Coll Med, Program Quantitat & Computat Biosci, Houston, TX USA
[4] Proteovant Therapeut, 2500 Renaissance Blvd, King Of Prussia, PA USA
关键词
Omics; Multi-omics; Visualization; Open-source; R; Bioinformatics; Genomics; Proteomics; Transcriptomics; Metabolomics; SET ENRICHMENT ANALYSIS; GENE;
D O I
10.1186/s12859-024-05743-4
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Background The results of high-throughput biology ('omic') experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and multiple analytical technologies, bioinformatic pipelines, and visualization preferences have emerged. Multiple software applications exist that support omic study exploration and/or archival. However, an opportunity remains for open-source software that can archive and present the results of omic analyses with broad accommodation of study-specific analytical approaches and visualizations with useful exploration features.Results We present OmicNavigator, an R package for the archival, visualization and interactive exploration of omic studies. OmicNavigator enables bioinformaticians to create web applications that interactively display their custom visualizations and analysis results linked with app-derived analytical tools, graphics, and tables. Studies created with OmicNavigator can be viewed within an interactive R session or hosted on a server for shared access.Conclusions OmicNavigator can be found at https://github.com/abbvie-external/OmicNavigator
引用
收藏
页数:10
相关论文
共 40 条
[11]   UpSetR: an R package for the visualization of intersecting sets and their properties [J].
Conway, Jake R. ;
Lex, Alexander ;
Gehlenborg, Nils .
BIOINFORMATICS, 2017, 33 (18) :2938-2940
[12]  
Core RT., 2022, R: A Language and Environment for Statistical Computing
[13]  
Irizarry RA, 2021, data analysis for the life sciences
[14]   Gene set enrichment analysis made simple [J].
Irizarry, Rafael A. ;
Wang, Chi ;
Zhou, Yun ;
Speed, Terence P. .
STATISTICAL METHODS IN MEDICAL RESEARCH, 2009, 18 (06) :565-575
[15]  
Isserlin Ruth, 2014, F1000Res, V3, P141, DOI 10.12688/f1000research.4536.1
[16]   Jupyter Notebooks-a publishing format for reproducible computational workflows [J].
Kluyver, Thomas ;
Ragan-Kelley, Benjamin ;
Perez, Fernando ;
Granger, Brian ;
Bussonnier, Matthias ;
Frederic, Jonathan ;
Kelley, Kyle ;
Hamrick, Jessica ;
Grout, Jason ;
Corlay, Sylvain ;
Ivanov, Paul ;
Avila, Damin ;
Abdalla, Safia ;
Willing, Carol .
POSITIONING AND POWER IN ACADEMIC PUBLISHING: PLAYERS, AGENTS AND AGENDAS, 2016, :87-90
[17]  
Law Charity W, 2016, F1000Res, V5, DOI 10.12688/f1000research.9005.3
[18]   voom: precision weights unlock linear model analysis tools for RNA-seq read counts [J].
Law, Charity W. ;
Chen, Yunshun ;
Shi, Wei ;
Smyth, Gordon K. .
GENOME BIOLOGY, 2014, 15 (02)
[19]   UpSet: Visualization of Intersecting Sets [J].
Lex, Alexander ;
Gehlenborg, Nils ;
Strobelt, Hendrik ;
Vuillemot, Romain ;
Pfister, Hanspeter .
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2014, 20 (12) :1983-1992
[20]   ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data [J].
Liu, Xian ;
Xu, Kaikun ;
Tao, Xin ;
Yin, Ronghua ;
Ren, Guangming ;
Yu, Miao ;
Li, Changyan ;
Chen, Hui ;
Zhao, Ke ;
Xiang, Shensi ;
Gao, Huiying ;
Bo, Xiaochen ;
Chang, Cheng ;
Yang, Xiaoming .
NUCLEIC ACIDS RESEARCH, 2022, 50 (W1) :W312-W321