omicsViewer - Interactive and explorative visualization of
SummarizedExperssionSet or ExpressionSet using omicsViewer
omicsViewer visualizes ExpressionSet (or
SummarizedExperiment) in an interactive way. The omicsViewer
has a separate back- and front-end. In the back-end, users need
to prepare an ExpressionSet that contains all the necessary
information for the downstream data interpretation. Some extra
requirements on the headers of phenotype data or feature data
are imposed so that the provided information can be clearly
recognized by the front-end, at the same time, keep a minimum
modification on the existing ExpressionSet object. The pure
dependency on R/Bioconductor guarantees maximum flexibility in
the statistical analysis in the back-end. Once the
ExpressionSet is prepared, it can be visualized using the
front-end, implemented by shiny and plotly. Both features and
samples could be selected from (data) tables or graphs (scatter
plot/heatmap). Different types of analyses, such as enrichment
analysis (using Bioconductor package fgsea or fisher's exact
test) and STRING network analysis, will be performed on the fly
and the results are visualized simultaneously. When a subset of
samples and a phenotype variable is selected, a significance
test on means (t-test or ranked based test; when phenotype
variable is quantitative) or test of independence (chi-square
or fisher’s exact test; when phenotype data is categorical)
will be performed to test the association between the phenotype
of interest with the selected samples. Additionally, other
analyses can be easily added as extra shiny modules. Therefore,
omicsViewer will greatly facilitate data exploration, many
different hypotheses can be explored in a short time without
the need for knowledge of R. In addition, the resulting data
could be easily shared using a shiny server. Otherwise, a
standalone version of omicsViewer together with designated
omics data could be easily created by integrating it with
portable R, which can be shared with collaborators or submitted
as supplementary data together with a manuscript.
