iSEE

iSEE provides visualization and exploration of high-throughput sequencing, transcriptomics, and proteomics data stored in SummarizedExperiment objects within the R/Bioconductor ecosystem.

Key Features:

• SummarizedExperiment support: Operates directly on data stored in SummarizedExperiment objects.
• R/Bioconductor integration: Integrates with numerous R/Bioconductor packages.
• Broad data applicability: Applies to various high-throughput assay data including sequencing, transcriptomics, and proteomics.
• Dynamic plot linking: Provides dynamic linking between plots to connect different visual representations of data.
• Metadata and results integration: Enables simultaneous examination of metadata and analysis results.
• Code tracking: Records code to support reproducibility of analyses.
• Large-dataset visualization: Supports exploration and visualization of large biological datasets from high-throughput assays.

Scientific Applications:

• Transcriptomics data exploration: Used to visualize and interrogate transcriptomics datasets.
• Proteomics data exploration: Used to visualize and interrogate proteomics datasets.
• Sequencing data interpretation: Applied to the interpretation of sequencing-derived high-throughput data.
• Reproducible analysis workflows: Supports reproducible reporting and tracking of analysis code.

Methodology:

Implemented within the R/Bioconductor ecosystem and operating on SummarizedExperiment objects, iSEE uses Shiny, provides dynamic linked plots, records code for reproducibility, and integrates with other Bioconductor packages.