Dandelion

Dandelion analyzes single-cell adaptive immune receptor sequencing (scVDJ-seq) data to characterize V(D)J repertoires and infer lymphocyte developmental trajectories.

Key Features:

• Improved V(D)J Contig Annotation: Provides refined annotations of V(D)J contigs, identifying productive and nonproductive rearrangements and partially spliced contigs.
• AIR Feature Space Creation: Constructs an adaptive immune receptor (AIR) feature space to enable differential V(D)J usage analysis and pseudotime trajectory inference.
• Trajectory Inference and Lineage Commitment Analysis: Aligns developmental trajectories of thymic double-positive T cells to mature single-positive CD4 and CD8 T cells to predict factors associated with lineage commitment.

Scientific Applications:

• Thymic T Cell Development: Supports analysis of thymic development trajectories, including alignment of double-positive T cells with mature single-positive CD4 and CD8 T cells.
• B1 Cell and ILC/NK Cell Development: Applied to study the origins of human B1 cells and the development of innate lymphoid cells (ILCs) and natural killer (NK) cells.

Methodology:

Integrates scVDJ-seq with single-cell RNA sequencing data and applies standard V(D)J analysis workflows at the single-cell level, including refined contig annotation, construction of an AIR feature space, differential V(D)J usage analysis, pseudotime trajectory inference, and alignment of developmental trajectories for lineage-commitment analysis.