Platypus

Platypus integrates lymphocyte single-cell immune repertoires with transcriptomic data to enable joint analysis of adaptive immune receptor (VDJ) repertoires and gene expression for molecular profiling of B and T lymphocytes.

Key Features:

• Integrated Repertoire and Transcriptome Analysis: Integrates adaptive immune receptor (VDJ) repertoires with single-cell gene expression to link B cell receptor (BCR) and T cell receptor (TCR) sequences to transcriptional states.
• Repertoire Quantification: Quantifies germline gene usage, clonal expansion, and somatic hypermutation and supports inference of antigen-specificity.
• Automated Analytical Framework: Implements unsupervised clustering, gene expression analysis, and gene ontology mapping to characterize transcriptional states.
• Support for VDJ and GEX Libraries: Handles VDJ and GEX single-cell libraries, enabling analysis of repertoires alone or combined with transcriptomes.

Scientific Applications:

• Clonal and Transcriptional Profiling: Characterizes clonal expansion and transcriptional profiles of lymphocytes across diverse disease contexts.
• COVID-19 Convalescent Immune Analysis: Analyzes single-cell immune repertoires and transcriptomes from B and T cells in convalescent COVID-19 patients to reveal repertoire features and transcriptional profiles of clonally expanded lymphocytes.

Methodology:

Processes high-throughput single-cell sequencing (scSeq) data and applies unsupervised clustering, gene expression analysis, and gene ontology mapping.