Tutorial is available here Ĭoming in the next releases: CDR3 amino acid physical and chemical properties assessment, mutation networks. K-mer distribution measures and statistics. Tracking of clonotypes across time points, widely used in vaccination and cancer immunology domains. Differentiated Technology: Atreca’s proprietary Immune Repertoire Capture (IRC) technology, informed and enabled by deep immunology expertise and dedicated infrastructure, accurately generates natively paired heavy and light chain sequences of the antibodies expressed by particular single B cells isolated from patient samples. Immune repertoire capture, which leverages next-generation sequencing, identifies new antibodies that have utility themselves and that define the targets of. Tutorial is available here ĭiversity evaluation (ecological diversity index, Gini index, inverse Simpson index, rarefaction analysis).

Gene usage estimation (correlation, Jensen-Shannon Divergence, clustering). Repertoire overlap analysis (common indices including overlap coefficient, Jaccard index and Morisita’s overlap index). Immune repertoire is defined as the sum of T cell receptors and B cell receptors (also named immunoglobulin) that makes the organism's adaptive immune system. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). The diversity of T and B cells in terms of their receptor sequences is huge in the vertebrate's immune system and provides broad protection against the vast diversity of pathogens. Most methods are incorporated in a couple of main functions with clear naming-no more remembering dozens and dozens of functions with obscure names. The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire.

Works on any data source you are comfortable with: R data frames, data tables from data.table, databases like MonetDB, Apache Spark data frames via sparklyr īeginner-friendly. Supports all popular TCR and BCR analysis and post-analysis formats, including single-cell data: ImmunoSEQ, IMGT, MiTCR, MiXCR, MiGEC, MigMap, VDJtools, tcR, AIRR, 10XGenomics, ArcherDX. The package automatically detects the format of your files-no more guessing what format is that file, just pass them to the package Antibody repertoire sequencing is a powerful tool for studying the development of adaptive immune responses. Fast and easy manipulation of immune repertoire data:

Immune repertoire capture standfod