Garnett

Garnett annotates cell types in single-cell transcriptional profiling and single-cell chromatin accessibility datasets using an interpretable hierarchical markup language that specifies cell type-specific genes.

Key Features:

• Rapid Annotation: Automates cell type annotation to accelerate a process that is traditionally manual and time-consuming.
• Hierarchical Markup Language: Employs an interpretable hierarchical markup language to define cell type-specific gene markers and hierarchical relationships among cell types.
• Data Modality Support: Classifies cells in both single-cell transcriptional profiling and single-cell chromatin accessibility datasets.
• Cross-Dataset Compatibility: Performs classification across diverse datasets derived from tissue samples and whole organisms.
• Cross-Species Application: Supports the classification of cell types across different species.

Scientific Applications:

• Single-cell genomics: Annotating cell types in single-cell transcriptional and chromatin accessibility studies to enable interpretation of cellular composition and heterogeneity.
• Comparative cell type mapping: Enabling cross-dataset and cross-species mapping of cell types across tissue samples and whole organisms.
• Cellular heterogeneity and process analysis: Facilitating investigation of complex biological processes at the cellular level through annotated single-cell profiles.

Methodology:

Garnett uses an interpretable hierarchical markup language to specify cell type-specific genes and classify cells in single-cell transcriptional and chromatin accessibility datasets.