UCSCXenaShiny

UCSCXenaShiny facilitates retrieval, normalization, integration, and visualization of large-scale public cancer and biomedical omics datasets hosted on UCSC Xena, including TCGA, ICGC, TARGET, GTEx, and CCLE, for comparative and statistical analyses.

Key Features:

• Data sources: Accesses public datasets hosted on UCSC Xena, including TCGA, ICGC, TARGET, GTEx, and CCLE.
• Data retrieval and exploration: Retrieves datasets from UCSC Xena data hubs to support dataset exploration.
• Module-based analysis framework: Provides integrated analysis modules for processing and visualizing retrieved datasets.
• Data normalization and integration: Normalizes and integrates datasets to enable combining, linking, filtering, and downloading across studies.
• Visualization: Produces visualizations to support comparative and statistical analysis of omics data.
• Scalability: Employs an architecture designed to handle large volumes of data efficiently.

Scientific Applications:

• Cancer genomics and multi-omics studies: Facilitates analysis of large-scale cancer omics datasets such as TCGA, ICGC, and TARGET.
• Comparative and cross-study analyses: Enables combining and comparing data across studies and cohorts, including comparisons with GTEx and CCLE.
• Statistical modeling and visualization: Supports workflows from basic data exploration to advanced statistical modeling and visualization of omics data.

Methodology:

Builds upon UCSCXenaTools for data retrieval and employs an architecture designed to handle large volumes of data efficiently.