Example of a principal coordinate analysis based on cosine distances on IGHV gene usage distributions of 42 samples.

<p>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.</p

Example of a comparison of Gini indices of three samples.

<p>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.</p

<i>bcRep</i>: R Package for Comprehensive Analysis of B Cell Receptor Repertoire Data

<div><p>Immunoglobulins, as well as T cell receptors, play a key role in adaptive immune responses because of their ability to recognize antigens. Recent advances in next generation sequencing improved also the quality and quantity of individual B cell receptors repertoire sequencing. Unfortunately, appropriate software to exhaustively analyze repertoire data from NGS platforms without limitations of the number of sequences are lacking. Here we introduce a new R package, <i>bcRep</i>, which offers a platform for comprehensive analyses of B cell receptor repertoires, using IMGT/HighV-QUEST formatted data. Methods for gene usage statistics, clonotype classification, as well as diversity measures, are included. Furthermore, functions to filter datasets, to do summary statistics about mutations, as well as visualization methods, are available. To compare samples in respect of gene usage, diversity, amino acid proportions, similar sequences or clones, several functions including also distance measurements, as well as multidimensional scaling methods, are provided.</p></div

Example of a comparison of diversities of CDR3 sequences in two samples.

<p>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.</p

Conversion of specific diversity indices to true diversity indices [13].

<p>Conversion of specific diversity indices to true diversity indices [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161569#pone.0161569.ref013" target="_blank">13</a>].</p

Example of an analysis of gene/gene combinations.

<p>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.</p

Comparison of the different B cell receptor repertoire analysis tools and <i>bcRep</i>.

<p>Comparison of the different B cell receptor repertoire analysis tools and <i>bcRep</i>.</p

Example of an analysis of replacement mutations.

<p>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.</p

Functions of the <i>bcRep</i> package and their description.

<p>Functions of the <i>bcRep</i> package and their description.</p

Example of an analysis of CDR3 amino acid sequence length distribution.

<p>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).</p