Table 1.
Comparison of the different B cell receptor repertoire analysis tools and bcRep.
Table 2.
Functions of the bcRep package and their description.
Fig 1.
Example of an analysis of gene/gene combinations.
A color coded heatmap represents the relative abundance of IGHV and IGHD combinations for a selected set of sequences. Bright colors represent low proportions, darker ones high proportions. Dendrograms represent hierarchical clustering of genes.
Fig 2.
Example of an analysis of replacement mutations.
Percentages of replacement mutations from one amino acid to another are color coded. Darker colors represent higher percentages, compared to bright colors. The amino acids of the germline sequence are shown in rows, the mutated ones in columns. The orange dots represent amino acid changes that result also in a hydropathy change.
Fig 3.
Example of an analysis of CDR3 amino acid sequence length distribution.
a) Percentages (y-axis) of different CDR3 sequence lengths (x-axis) (upper figure). b) Percentages (y-axis) of productive (orange) and unproductive (blue) sequences per CDR3 sequence length (x-axis) (lower figure).
Table 3.
Conversion of specific diversity indices to true diversity indices [13].
Fig 4.
Example of a comparison of diversities of CDR3 sequences in two samples.
Diversity indices of order one are given on the y-axis, CDR3 lengths (amino acids) are on the x-axis. Samples are color coded (blue and red). Dots represent mean diversities of all CDR3 sequences of given length; bars represent standard deviation. Diversity is alike in both samples, except for longer sequences (with a length of 21 to 26 amino acids), where CDR3’s of sample A are more diverse than those of sample B.
Fig 5.
Example of a comparison of Gini indices of three samples.
Gini indices are displayed on the y-axis, samples are on the x-axis. The Gini index can lie between zero and one. An index of zero represents a clone set of equally distributed clones, all having the same size. A Gini index of one would point to a set including only one clone with many sequences.
Fig 6.
Example of a principal coordinate analysis based on cosine distances on IGHV gene usage distributions of 42 samples.
The dots are color coded for two groups. First (x-axis) and second (y-axis) axes are plotted and the variances explained by these axes are given.