BatchServer

BatchServer corrects and evaluates batch effects in omics datasets using autoComBat, PVCA, and UMAP.

Key Features:

• autoComBat: Implements autoComBat, a modified version of ComBat, for batch effect correction.
• ComBat compatibility: Uses the statistical framework of ComBat as the basis for automated batch adjustment.
• PVCA: Quantifies variance attributable to batch effects using Principal Variance Component Analysis (PVCA).
• UMAP: Applies Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and visualization of high-dimensional omics data.
• Implementation: Implemented using R and Shiny.

Scientific Applications:

• Proteomics: Evaluation and correction of batch effects in proteomics datasets.
• Transcriptomics: Evaluation and correction of batch effects in transcriptomic datasets.

Methodology:

Implements autoComBat (a modified ComBat) for batch correction, uses PVCA to quantify batch-attributable variance, and uses UMAP for dimensionality reduction and visualization.