HDCytoData

HDCytoData provides curated high-dimensional flow cytometry and mass cytometry (CyTOF) benchmark datasets formatted for Bioconductor SummarizedExperiment and flowSet objects to support method development and benchmarking in cytometry.

Key Features:

• Extensive Dataset Collection: Includes a curated collection of publicly available high-dimensional flow cytometry and mass cytometry (CyTOF) benchmark datasets for validating clustering and differential-analysis methods.
• Standardized Data Formats: Datasets are provided as SummarizedExperiment and flowSet Bioconductor object formats.
• Comprehensive Metadata Inclusion: Each dataset contains embedded metadata within the Bioconductor objects to enable contextual and reproducible analyses.
• Data Distribution via ExperimentHub: Datasets are provided through Bioconductor's ExperimentHub platform.
• Extensibility for Contributions: The package supports addition of new datasets by contributors to expand the benchmark repository.

Scientific Applications:

• Method Evaluation: Assess performance of clustering and differential analysis algorithms on high-dimensional cytometry data.
• Reproducibility Studies: Use embedded metadata to perform reproducibility and verification studies of analytical results.
• Educational Applications: Provide real-world cytometry datasets for teaching data analysis techniques in bioinformatics and cytometry.

Methodology:

Publicly available high-dimensional cytometry datasets are collected and organized into SummarizedExperiment and flowSet Bioconductor objects and distributed via ExperimentHub.