immunarch

immunarch analyzes T-cell receptor (TCR) and B-cell receptor (BCR) repertoire sequencing data to quantify diversity, identify clonotypes, perform sequence-level comparisons, and visualize immune-repertoire features for immunological research.

Key Features:

• Implementation: An R package providing functions for repertoire-level and sequence-level analysis of TCR and BCR data.
• Comprehensive analysis: Calculates diversity metrics, performs clonotype identification, and supports sequence alignment for TCR/BCR repertoires.
• Data integration: Supports integration of multiple input data formats and sources for combined repertoire analyses.
• Visualization: Generates plots and visual summaries to explore repertoire diversity, clonality, and sequence features.

Scientific Applications:

• Immune response profiling: Characterizes TCR and BCR diversity and clonality in studies of infection, vaccination, or disease.
• Immunotherapy research: Supports analysis of receptor repertoires relevant to development and evaluation of immunotherapies.
• Comparative repertoire analysis: Enables cohort- or sample-level comparisons of clonotype distributions and diversity metrics.
• Hypothesis generation: Uses sequence- and repertoire-level visualizations to inform downstream experimental or analytical investigations.

Methodology:

Immunarch implements computation of diversity metrics, clonotype identification, sequence alignment, data-format integration, and visualization functions within the R environment.