VDJdive

VDJdive provides functions for handling and analyzing immune receptor repertoire data produced by the CellRanger V(D)J pipeline, including reading data into R, merging with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots.

Key Features:

• Data Import: Reads immune receptor repertoire data into R from the CellRanger V(D)J pipeline output.
• Single-Cell Integration: Merges V(D)J data with paired single-cell data.
• Clonotype Quantification: Quantifies clonotype abundances using the E-M Algorithm for clonotype assignment along with other methods.
• Ambiguous Cell Utilization: Makes use of ambiguous cells for improved clonotype quantification.
• Diversity Analysis: Calculates diversity metrics for immune receptor repertoires.
• Visualization: Produces common plots for repertoire data analysis.

Scientific Applications:

• Immune Repertoire Analysis: Analyzes immune receptor repertoire data from 10X V(D)J sequencing experiments.
• Clonotype Assignment: Assigns clonotypes using the E-M Algorithm to improve quantification accuracy with ambiguous cells.
• Single-Cell Immune Profiling: Integrates V(D)J repertoire information with paired single-cell transcriptomic data.
• Repertoire Diversity Assessment: Calculates diversity metrics to characterize immune receptor repertoire composition.

Methodology:

VDJdive implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.