rdi (original) (raw)

The RDI package is part of the Immcantationanalysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides an methods for visualizing and calculating the Repertoire Dissimilarity Index (RDI).

The Repertoire Dissimilarity Index is a non-parametric method for directly comparing sequencing repertoires, with the goal of rigorously quantifying differences in V, D, and J gene segment utilization. This method uses a bootstrapped subsampling approach to account for variance in sequencing depth, and, coupled with a data simulation approach, allows for direct quantification of the average variation between repertoires.

For help and questions please contact the Immcantation Groupor use the issue tracker.

Dependencies¶

Imports: beanplot, gplots, pdist, stringr
Suggests: knitr, ggplot2

Christopher Bolen (aut, cre)
Florian Rubelt (aut)
Jason Vander Heiden (aut)

Citing¶

To cite the RDI method in publications use:

Bolen CR, Rubelt F, Vander Heiden JA, Davis MM. The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires. BMC Bioinformatics. 2017 Mar 7;18(1):155.

A BibTeX entry for LaTeX users is

@Article{, title = {The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires}, author = {Christopher R Bolen and Florian Rubelt and Jason A {Vander Heiden} and Mark M Davis}, journal = {BMC Bioinformatics}, year = {2017}, volume = {18}, pages = {155}, }