/MiXCR_VDJtools

TCR repertoire analysis from bulk RNA-Seq data

Primary LanguageShell

MiXCR_VDJtools

TCR repertoire analysis from bulk RNA-Seq data

Pipeline structure

  • align

    $ bash mixcr.sh

  • two rounds of assemblePartial, extend, assemble and export to human readable format

    $ bash mixcr_processing.sh

  • conversion into vdj format (requires metafile)

    $ bash vdjtools.sh

Clonality

  • proportion of singletons, doubletons and high-order clones within each sample

    $ bash quantile_stats.sh

  • clonality measurements (requires metafile)

    $ bash diversity_stats.sh

Overlap analysis

  • simultaneous between all samples (requires metafile)

    $ bash vdj_tools_overlap_strict.sh

  • one by one

    $ bash vdj_tools_overlap_one_by_one.sh