Analysis of bulk and single-cell TCR and BCR libraries
TCR_demultiplex.sh, BCR_demultiplex.sh: use MiGEC and MiXCR to demultiplex paired-end reads from Illumina sequencing and align TCRs or BCRs.
readStats.py: Determines for single-cell plateseq experiment, such as FACS-sorted single cells, the clonal read count per well.
blankProportion.py: determines the proportion of blank reads as a function of clone read count. Useful for determining the optimal read count cutoff.
CDRcounts.py: Count CDR3 occurrence
pgen.py: Determine generation probability of CDR3a and CDR3b for a list of TCRs
