bio-tcr-bcr-analysis-immcantation-analysis

Load and Format Data

Goal: Import AIRR-formatted repertoire data into the Immcantation framework for downstream analysis.

Approach: Read Change-O/AIRR tab-delimited files into R data frames with required V(D)J annotation columns.

library(alakazam)
library(shazam)
library(dplyr)

## Clonal Clustering

**Goal:** Group B cell sequences into clonal lineages based on junction sequence similarity.

**Approach:** Apply hierarchical clustering on nucleotide distance of junction regions with a threshold-based cutoff.

```r
library(scoper)

## Threshold typically 0.15-0.2 (15-20% nucleotide distance)

db <- hierarchicalClones(
    db,
    threshold = 0.15,
    method = 'nt',
    linkage = 'single'
)