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vdjtools-analysis

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Computes immune-repertoire diversity, clonal structure, overlap, and segment usage from TCR/BCR clonotype tables with VDJtools (immunarch as the modern R alternative). Use when deciding which diversity estimator answers a question (q=0 observed richness/chao1/chaoE, q=1 shannonWienerIndex, q=2 inverseSimpson as a Hill profile); normalizing sequencing depth before any cross-sample claim (DownSample or the resampled CalcDiversityStats table); choosing an overlap metric (depth-robust MorisitaHorn/F2 vs depth-biased Jaccard/public counts) and a clonotype match key (-i nt/aa, +/-V/J); summarizing clonality as 1 - normalizedShannonWienerIndex; reading spectratype and V-J usage under primer bias; interpreting public clonotypes; and choosing VDJtools (stable Java CLI) vs immunarch (active tidy R).

When to use

• Computing immune-repertoire diversity
• Analyzing clonal structure
• Quantifying repertoire overlap
• Summarizing segment usage
• Normalizing sequencing depth
• Choosing diversity estimators
• Interpreting public clonotypes
• Comparing VDJtools vs immunarch

When not to use

• Processing FASTQ files
• Pre-analysis steps

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