Seurat

Seurat performs quality control, analysis, integration, and exploration of single-cell RNA sequencing (RNA-seq) and multimodal single-cell data to identify and interpret sources of cellular heterogeneity.

Key Features:

• Quality control (QC): Implements QC workflows for single-cell RNA-seq data.
• Analysis and exploration: Provides analysis and exploratory functions to identify and interpret sources of heterogeneity in single-cell transcriptomic measurements.
• Multimodal data integration: Integrates diverse types of single-cell data to enable multimodal analyses and define cellular identities beyond transcriptomes.
• Weighted-nearest neighbor (WNN) analysis: Implements an unsupervised weighted-nearest neighbor framework that assesses and assigns relative utility to each data modality within a cell.
• Reference atlas construction: Constructs multimodal reference atlases from complex single-cell datasets.
• Reference mapping: Supports rapid mapping of new datasets against established references for comparative interpretation.
• CITE-seq application: Applied to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with a 228-antibody panel to build a multimodal reference atlas.
• Cell-subpopulation identification: Enables identification and validation of previously unreported lymphoid subpopulations.

Scientific Applications:

• Cellular heterogeneity analysis: Identify and interpret sources of cellular heterogeneity in single-cell RNA-seq and multimodal datasets.
• Multimodal reference atlases: Construct multimodal reference atlases from datasets such as CITE-seq PBMC collections.
• Discovery of cell subpopulations: Discover and validate novel lymphoid subpopulations within immune datasets.
• Reference-based interpretation: Map new datasets to references to interpret biological phenomena including immune responses to vaccination and COVID-19.

Methodology:

Implements an unsupervised weighted-nearest neighbor (WNN) analysis that assigns relative utility to each data modality to enable integrative multimodal analyses, construct multimodal reference atlases, and map new datasets to established references.