HPAanalyze

HPAanalyze retrieves, analyzes, and visualizes data from the Human Protein Atlas.

Key Features:

• Data Import and Export: Imports, subsets, and exports downloadable datasets from the Human Protein Atlas.
• Visualization: Generates visualizations of downloadable datasets for exploratory analysis.
• XML File Processing: Works with individual XML files from the Human Protein Atlas.
• Image Download: Downloads all staining images of interest from the Human Protein Atlas.

Scientific Applications:

• Gene Set Analysis: Enables data analysis of gene sets rather than individual proteins from the Human Protein Atlas.
• Cancer Protein Investigation: Identifies proteins altered in diseases such as glioblastoma, including confirmation of Epidermal Growth Factor Receptor elevation and Phosphatase and Tensin Homolog loss.
• Pathway Discovery: Supports investigation of biological pathways such as the GTP Cyclohydrolase I/Tetrahydrobiopterin pathway.

Methodology:

HPAanalyze integrates into the R workflow with the tidyverse framework and can be used in combination with Bioconductor packages.