UCSCXenaTools

UCSCXenaTools provides programmatic access to genomics and multi-omics data hosted on UCSC Xena for integration and analysis of cancer and single-cell (scRNA-seq) datasets.

Key Features:

• Data Integration: Integrates data from UCSC Xena turn‑key Hubs including TCGA, ICGC, TARGET, GTEx, and CCLE with datasets normalized for compatibility.
• Data Exploration and Filtering: Offers functions to explore and filter large-scale genomic and single-cell RNA-seq datasets to extract relevant subsets.
• Download Capabilities: Retrieves and downloads filtered or selected datasets directly from the UCSC Xena platform.

Scientific Applications:

• Cancer Research: Accesses and analyzes comprehensive TCGA and ICGC multi-omics datasets to study genomic alterations in cancer.
• Single-cell Analysis: Utilizes scRNA-seq data to investigate cellular heterogeneity and gene expression patterns.
• Translational Studies: Leverages GTEx and TARGET datasets for genotype-phenotype investigations and development of targeted therapies.

Methodology:

Implemented as an R package that connects to UCSC Xena Hubs to query, integrate (normalized), explore, filter, and download public genomics and multi-omics datasets.