bio-tcr-bcr-analysis-vdjtools-analysis

To compute immune repertoire diversity metrics like Shannon and Chao1 from TCR data, upload MiXCR or VDJtools-compatible input files. The workflow processes your samples to calculate diversity indices, sample overlap, and spectratype outputs.

You can track clonotypes over time across longitudinal multi-sample studies by processing your VDJtools-compatible files with metadata. This identifies shared or public clonotypes and visualizes clonal dynamics across different conditions and time points.

Yes, you can analyze V and J segment usage and spectratypes for BCR repertoires. The workflow processes BCR data alongside TCR data to generate segment-usage outputs and spectratype distributions for comprehensive immune repertoire comparisons.

To compare immune repertoire overlap across multiple conditions, you need MiXCR or VDJtools-compatible input files and a metadata file. Java is also required to run the VDJtools environment for processing the multi-sample comparisons.

To parse VDJtools outputs for downstream plotting in Python, the workflow provides Python parsing scripts. These scripts process the diversity, overlap, and spectratype outputs to enable custom visualizations of your immune repertoire data.

The best way to compare clonal expansion between different sample groups is using a multi-sample metadata file with your VDJtools-compatible inputs. This enables reproducible comparisons of clonal dynamics, diversity, and overlap across defined conditions.