esetVis

esetVis visualizes Bioconductor ExpressionSet and SummarizedExperiment objects to produce static and interactive plots for exploring high-throughput genomics and molecular biology data.

Key Features:

• Supported input objects: Accepts Bioconductor ExpressionSet and SummarizedExperiment objects as direct inputs.
• Visualization techniques: Implements spectral mapping, t-distributed stochastic neighbor embedding (t-SNE), and linear discriminant analysis (LDA) for dimensionality reduction and pattern discovery.
• Static plotting: Generates static visualizations using the ggplot2 package.
• Interactive plotting: Produces interactive visualizations via ggvis and rbokeh.
• R and Bioconductor interoperability: Operates within the R environment and interoperates with other Bioconductor packages.

Scientific Applications:

• Genomics and molecular biology: Visualizes gene expression data to support identification of differentially expressed genes, exploration of biological pathways, and assessment of sample heterogeneity.
• Interdisciplinary high-throughput data analysis: Enables visualization-driven analysis of high-throughput datasets across different research fields.

Methodology:

Operates in R within the Bioconductor ecosystem on ExpressionSet and SummarizedExperiment objects, using ggplot2 for static plots, ggvis and rbokeh for interactive plots, and applying spectral mapping, t-SNE, and LDA for dimensionality reduction and visualization.