SurfR

SurfR provides a streamlined end-to-end workflow for computationally identifying surface protein-coding genes from expression data.

Key Features:

• Data Retrieval: Systematically downloads expression data from GEO and TCGA databases or accepts user-provided data.
• Differential Gene Expression: Performs DGE analysis on bulk RNA-seq data across conditions.
• Meta-analysis: Integrates multiple datasets for combined analysis.
• Enrichment Analysis: Performs descriptive enrichment analysis with accompanying plots.
• Target Identification: Identifies targetable proteins for a condition of interest.

Scientific Applications:

• Biomarker Discovery: Identifies condition-specific cell-surface proteins that may serve as biomarkers for detecting cells of interest in tissues or body fluids.
• Therapeutic Target Identification: Identifies surface proteins that are often targets of pharmaceutical agents and hold promise for treatment development.
• Clinical Research: Supports diagnosis, prognosis, and evaluation of therapy response through identification of distinct sets of cell-surface proteins in healthy versus diseased cells.

Methodology:

The package performs systematic expression data retrieval from public databases, differential gene expression across conditions, integration of datasets, enrichment analysis, identification of targetable proteins on a condition of interest, and data visualization.