OmicNavigator: Open-source Software for the Exploration, Visualization, and Archival of Omic Studies

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2024 Apr 24

PMID 38658834

Authors

Terrence R Ernst

John D Blischak

Paul Nordlund

Joe Dalen

Justin Moore

Akshay Bhamidipati

Pankaj Dwivedi

Joe LoGrasso

Marco Rocha Curado

Brett Warren Engelmann

Affiliations

Soon will be listed here.

Abstract

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.

References

Wu D, Lim E, Vaillant F, Asselin-Labat M, Visvader J, Smyth G . ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics. 2010; 26(17):2176-82. PMC: 2922896. DOI: 10.1093/bioinformatics/btq401. View

Irizarry R, Wang C, Zhou Y, Speed T . Gene set enrichment analysis made simple. Stat Methods Med Res. 2010; 18(6):565-75. PMC: 3134237. DOI: 10.1177/0962280209351908. View

Liu X, Xu K, Tao X, Yin R, Ren G, Yu M . ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data. Nucleic Acids Res. 2022; 50(W1):W312-W321. PMC: 9252728. DOI: 10.1093/nar/gkac399. View

Ritchie M, Phipson B, Wu D, Hu Y, Law C, Shi W . limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015; 43(7):e47. PMC: 4402510. DOI: 10.1093/nar/gkv007. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister A . FAIRsharing as a community approach to standards, repositories and policies. Nat Biotechnol. 2019; 37(4):358-367. PMC: 6785156. DOI: 10.1038/s41587-019-0080-8. View

Mullan K, Bramberger L, Munday P, Goncalves G, Revote J, Mifsud N . ggVolcanoR: A Shiny app for customizable visualization of differential expression datasets. Comput Struct Biotechnol J. 2021; 19:5735-5740. PMC: 8551465. DOI: 10.1016/j.csbj.2021.10.020. View

Conway J, Lex A, Gehlenborg N . UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017; 33(18):2938-2940. PMC: 5870712. DOI: 10.1093/bioinformatics/btx364. View

Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M . WIlsON: Web-based Interactive Omics VisualizatioN. Bioinformatics. 2018; 35(6):1055-1057. PMC: 6419899. DOI: 10.1093/bioinformatics/bty711. View

10.

Wu D, Smyth G . Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res. 2012; 40(17):e133. PMC: 3458527. DOI: 10.1093/nar/gks461. View

11.

Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H . UpSet: Visualization of Intersecting Sets. IEEE Trans Vis Comput Graph. 2015; 20(12):1983-92. PMC: 4720993. DOI: 10.1109/TVCG.2014.2346248. View

12.

Isserlin R, Merico D, Voisin V, Bader G . Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. F1000Res. 2014; 3:141. PMC: 4103489. DOI: 10.12688/f1000research.4536.1. View

13.

Bouhaddou M, Memon D, Meyer B, White K, Rezelj V, Marrero M . The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020; 182(3):685-712.e19. PMC: 7321036. DOI: 10.1016/j.cell.2020.06.034. View

14.

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

15.

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

16.

Su S, Law C, Ah-Cann C, Asselin-Labat M, Blewitt M, Ritchie M . Glimma: interactive graphics for gene expression analysis. Bioinformatics. 2017; 33(13):2050-2052. PMC: 5870845. DOI: 10.1093/bioinformatics/btx094. View

17.

Law C, Chen Y, Shi W, Smyth G . voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014; 15(2):R29. PMC: 4053721. DOI: 10.1186/gb-2014-15-2-r29. View

18.

Bostock M, Ogievetsky V, Heer J . D³: Data-Driven Documents. IEEE Trans Vis Comput Graph. 2011; 17(12):2301-9. DOI: 10.1109/TVCG.2011.185. View

19.

Rue-Albrecht K, Marini F, Soneson C, Lun A . iSEE: Interactive SummarizedExperiment Explorer. F1000Res. 2018; 7:741. PMC: 6013759. DOI: 10.12688/f1000research.14966.1. View

20.

Naake T, Huber W . MatrixQCvis: shiny-based interactive data quality exploration for omics data. Bioinformatics. 2021; 38(4):1181-1182. PMC: 8796383. DOI: 10.1093/bioinformatics/btab748. View