Repertoire Dissimilarity Index

Methods for calculation and visualization of the Repertoire Dissimilarity Index. Citation: Bolen and Rubelt, et al (2017) .


RDI

The RDI package is part of the Immcantation analysis 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.

Contact

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

News

Version 1.0.0: May 1, 2018

Internal changes and extra documentation for submission to CRAN.

Some variable names changed for consistency:

  • n_iter changed to nIter
  • label.ladder changed to labelLadder
  • line.col changed to lineCol
  • fill.col changed to fillCol

Version 0.9.0: October 12, 2016

Initial public release.

Reference manual

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install.packages("rdi")

1.0.0 by Christopher Bolen, 2 years ago


http://rdi.readthedocs.io


Report a bug at https://bitbucket.org/cbolen1/rdicore/issues


Browse source code at https://github.com/cran/rdi


Authors: Christopher Bolen [aut, cre] , Florian Rubelt [aut] , Jason Vander Heiden [aut]


Documentation:   PDF Manual  


CC BY-SA 4.0 license


Imports beanplot, gplots, pdist, stringr

Suggests knitr, ggplot2


See at CRAN