R package is also distributed on
It only contains the
R code to analyse the clonotypes extracted by the
scripts for processing the raw sequences, which are to be downloaded as
From source repository
Install the requirements below, and then clone clonotypeR with git, then build and install the R module
git clone git://clonotyper.branchable.com/ clonotyper R CMD build clonotyper R CMD INSTALL clonotypeR_0.9.tar.gz # Adjust for the correct version number
See the example analysis of GSE35626 for a more detailed walkthrough.
- EMBOSS, to manipulate the reference sequences.
- BWA (Burrows-Wheeler Aligner), to identify the trimmed V segments.
- BioPerl (> 1.6.9), to translate the CDRs. Lower versions differ on how they translate incomplete last codons.
- R for creating expression tables and analysing them.