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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

-

-

+