TCR repertoire analysis from bulk RNA-Seq data
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align
$ bash mixcr.sh
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two rounds of assemblePartial, extend, assemble and export to human readable format
$ bash mixcr_processing.sh
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conversion into vdj format (requires metafile)
$ bash vdjtools.sh
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proportion of singletons, doubletons and high-order clones within each sample
$ bash quantile_stats.sh
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clonality measurements (requires metafile)
$ bash diversity_stats.sh
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simultaneous between all samples (requires metafile)
$ bash vdj_tools_overlap_strict.sh
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one by one
$ bash vdj_tools_overlap_one_by_one.sh