OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons

Table 1 Comparison of software for omics data visualization

Software	OmicLoupe	Perseus [7]	WIlsON [9]	ShinyOmics [8]	Intervene [10]
Web deployment	Yes	No	Yes	Yes	Yes
Open source	Yes	No	Yes	Yes	Yes
Platform independent installation	Yes	No	Yes	Yes	Yes
Container-based dependency management	Yes	No¹	Yes	Yes	No
Compare multiple datasets	Yes	Yes	No	Yes	Yes (overlap)
Correlations between datasets	Yes	Yes	No	No	Yes
Statistical calculations²	No	Yes	No	No	No
Overview plots (Box-plot, PCA, dendrograms)	Yes	Yes	Yes	Yes	No
Network visualization	No	Yes	No	Yes	No
Side-by-side comparisons³	Yes	No	No	No	No
Single-feature visualization⁴	Yes	Yes	Yes	No	No
Feature selection from visuals⁵	Yes	No	No	Limited	No
Overlap visualizations⁶	Yes	Limited	No	No	Yes
Fold-oriented analysis⁷	Yes	No	No	No	No
Absence/presence comparisons	Yes	Yes	No	No	No
Export publication ready figures (vector format)	Yes	Yes	Yes	Yes	Yes
Export reports and settings	Yes	Yes	Yes	No	No
Tutorial videos	Yes	Yes	No	No	No

Simplified overview of features in a selection of software solutions for omics data visualization
¹Installer provided
²“Yes” if calculation of statistical contrasts is performed interactively within the software, “No” if part of pre-processing is performed before loading data in the software
³Cross-comparison volcano plots or similar
⁴Detailed display of how individual measurements distribute over sample conditions
⁵Selection of subsets of features by direct interaction with the visuals. “Limited” if one type of visualization is provided, “Yes” for multiple types including interactive scatter-plots, and highlighting of subsections in overlap-plots with visualization of the selection
⁶“Limited” if only Venn. “Yes” if extended overlap representations such as UpSet plots
⁷Possibility to split visualizations to highlight features with similar or different abundance change directions in multiple comparisons

ISSN: 1471-2105