clonotypeR's workflow

This workflow summarises the different commands to run. Step-by-step examples using test data or the GSE35626 public dataset are also available for a more detailed explanation. See also the preprint of our application note deposited in bioRxiv.

Data preparation in the command line

Convert sequencer ouptut files from Sanger or 454 sequencers. Single-end Illumina sequence output can be used directly. Paired-end sequences need to be merged.

ClonotypeR is ran in two steps.

  • clonotypeR detect compares the sequences to a reference database of V segments.

  • clonotypeR extract searches for J segments in sequences where a V segment was found, extracts the CDR3s and reports the results in a table ready to be loaded in R.

See the manual page of clonotypeR for more details.

Data analysis in R

The R package can be loaded with the following command.


The file produced by clonotypeR extract is loaded by the read clonotypes(). Expression tables are calculated by the clonotype table(). These tables are the basis for the analysis, to compare clonotype profiles, cluster the samples, calculate overlaps, etc.

Alignment score histogram Scale-free distribution of the data Similar libraries group together Differential clonotype expression analysis

See the list of functions for more information.