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 | - | - | + |