Skip to main content

Advertisement

Table 1 Comparison of tcR package with other existing TR data analysis software

From: tcR: an R package for T cell receptor repertoire advanced data analysis

Subroutines\Software MiTCRViewer ViDJiL tcR
CDR3 sequence extraction and clonotype set building + (using MiTCR) + -
Sequence motif search + −/+ (exact match only) +
Descriptive statistics (number of reads, number of clonotype sets, gene usage) + + +
Number of shared clonotypes counting (with identical nucleotide or amino acid sequence) - - +
Repertoire similarity measures (Jaccard index, Morisita’s overlap index) - - +
Construction of shared clonotypes repertoires - - +
Jensen-Shannon divergence computing for analysis of gene usage - - +
PCA for analysis of gene usage - - +
Repertoire diversity analysis (diversity estimation, rarefaction analysis, etc.) - - +
Clonal abundance visualisation - + +
Histograms of gene distributions - + +
CDR3 length distribution visualisation - + +
Radar plots for visualisation of distribution similarity (e.g., Jensen-Shannon divergence among set of distributions of genes) - - +
Heatmaps for visualisation of repertoire similarity (e.g., number of shared clonotypes) - - +
In silico spectratyping + + +
Automatic report generation - - +
Artificial repertoire generation - - +