scTypeEval

scTypeEval provides tools to evaluate and validate cell type classifications in single-cell transcriptomics when ground truth labels are limited or unavailable.

Key Features:

• S4 Object Integration: Results are organized in an S4 object that integrates processed data, dimensional reductions, dissimilarity assays, and consistency metrics computed across samples.
• Preprocessing and Feature Selection: The workflow includes preprocessing and feature selection for single-cell transcriptomic data.
• Dimensional Reduction: Principal component analysis is performed as part of the analytical workflow.
• Dissimilarity Computation: Computation of dissimilarity matrices is supported for evaluating cell type relationships.
• Internal Validation Metrics: Internal validation metrics including silhouette-based summaries are computed.
• Visualization Utilities: Visualization utilities enable inspection of heatmaps and PCA plots.
• Single-Cell Container Support: Functions support common single-cell containers and enable comparison of clustering and labeling strategies across datasets.

Scientific Applications:

• Cell Type Classification Validation: scTypeEval evaluates and validates cell type classifications when ground truth labels are limited or unavailable.
• Cross-Dataset Comparison: The tool enables comparison of clustering and labeling strategies across datasets.
• Consistency Assessment: Consistency metrics are computed across samples to assess classification reliability.

Methodology:

The workflow includes preprocessing and feature selection, principal component analysis, computation of dissimilarity matrices, and internal validation metrics such as silhouette-based summaries.