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arda 2.38.4

  • Quickstart
  • Installation
  • Usage
  • Run within a CPU and memory budget
    • Recipes
    • Use cases and analysis guidelines
    • Single cell
    • Quality control
    • Samples split across files
    • Running on a cluster (SLURM)
    • Pipeline integration
    • Command reference
    • Output files and columns
    • Glossary
    • Benchmarks
    • Exporting the reference
    • Reference database build
    • API reference
    • How arda works
    • Productivity: productive, stop_codon, vj_in_frame
    • Error correction
    • Somatic hypermutation
    • D segments and tandem D-D
    • Personalized germline: genotype and call restriction
    • Recombination scenarios
  • GitHub
  • Quickstart
  • Installation
  • Usage
  • Run within a CPU and memory budget
  • Recipes
  • Use cases and analysis guidelines
  • Single cell
  • Quality control
  • Samples split across files
  • Running on a cluster (SLURM)
  • Pipeline integration
  • Command reference
  • Output files and columns
  • Glossary
  • Benchmarks
  • Exporting the reference
  • Reference database build
  • API reference
  • How arda works
  • Productivity: productive, stop_codon, vj_in_frame
  • Error correction
  • Somatic hypermutation
  • D segments and tandem D-D
  • Personalized germline: genotype and call restriction
  • Recombination scenarios
  • GitHub

Tutorial

  • Quickstart

How-to guides

  • Installation
  • Usage
  • Run within a CPU and memory budget
  • Recipes
  • Use cases and analysis guidelines
  • Single cell
  • Quality control
  • Samples split across files
  • Running on a cluster (SLURM)
  • Pipeline integration

Reference

  • Command reference
  • Output files and columns
  • Glossary
  • Benchmarks
  • Exporting the reference
  • Reference database build
  • API reference

Explanation

  • How arda works
  • Productivity: productive, stop_codon, vj_in_frame
  • Error correction
  • Somatic hypermutation
  • D segments and tandem D-D
  • Personalized germline: genotype and call restriction
  • Recombination scenarios
  • Overview: module code

All modules for which code is available

  • arda._database_fetch
  • arda._log
  • arda.adapter
  • arda.alleles
  • arda.annotate.candidates
  • arda.annotate.cigar
  • arda.annotate.contig
  • arda.annotate.dmap
  • arda.annotate.io
  • arda.annotate.mapper
  • arda.annotate.reference
  • arda.annotate.shortlist
  • arda.annotate.transfer
  • arda.cdr3fix
  • arda.cell
  • arda.cluster
  • arda.igblast
  • arda.mmseqs
  • arda.partition
  • arda.paths
  • arda.prefilter
  • arda.refbuild.build
  • arda.refbuild.combinations
  • arda.refbuild.imgt
  • arda.refbuild.segments
  • arda.refbuild.translate
  • arda.rnaseq._res
  • arda.rnaseq.assemble
  • arda.rnaseq.correct
  • arda.rnaseq.map
  • arda.rnaseq.pipeline
  • arda.scplot
  • arda.singlecell
  • arda.stats

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