iSEE

iSEE provides a general visual interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata, with direct compatibility with R/Bioconductor packages for analyzing high-throughput biological data.

Key Features:

• SummarizedExperiment Compatibility: Explores data stored in SummarizedExperiment objects, including row- and column-level metadata.
• SingleCellExperiment Support: Provides special attention to single-cell data in SingleCellExperiment objects with visualization of dimensionality reduction results.
• Dynamic Linking: Supports transmission of selections between plots and tables for simultaneous examination of (meta)data and analysis results.
• Reproducibility: Implements code tracking to record actions for reproducibility.
• Initialization Options: Supports interactive or programmatic initialization of the interface.
• State Preservation: Enables preservation of app state across sessions.
• Extensibility: Allows extension to new panel types via S4 classes.

Scientific Applications:

• Transcriptomics Data Exploration: Applies to exploration of real transcriptomics data sets from high-throughput assays such as sequencing.
• Proteomics Data Exploration: Applies to exploration of real proteomics data sets.
• Single-Cell Analysis: Visualizes dimensionality reduction results for single-cell data in SingleCellExperiment objects.

Methodology:

iSEE creates an interactive Shiny-based graphical user interface and implements dynamic linking between plots and tables with code tracking for reproducibility.