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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.

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

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Version

Install

install.packages('rdi')

Monthly Downloads

123

Version

1.0.0

License

CC BY-SA 4.0

Last Published

May 7th, 2018

Functions in rdi (1.0.0)

calcRDI

Calculate repertoire distances
rdi

Calculate RDI dissimilarity matrix
rdiAxis

RDI Axis annotation function
plotRDIladder

RDI ladder plotting function
convertRDI

Convert RDI measures
rdiLadder

RDI ladder
calcVDJcounts

Calculate repertoire counts
rdiModel

RDI Models