Logo
  • Overview
  • Installation
  • Required database
  • External softwares
  • Basic requirements
  • Acknowledgements

Tutorial:

  • Pre-processing
  • Filtering
  • BCR clustering and visualization
  • Running from R

API:

  • Preprocessing: pp
  • Preprocessing (external): pp.external
  • Tools: tl
  • Plotting: pl
  • Utilities: utl
dandelion
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  • Welcome to dandelion’s documentation!
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Welcome to dandelion’s documentation!¶

  • Overview
  • Installation
  • Required database
  • External softwares
  • Basic requirements
  • Acknowledgements

Tutorial:

  • Pre-processing
    • Foreword
    • Step 1: Formatting the headers of the cellranger fasta file
    • Step 2: Reannotate the V/D/J genes with igblastn
    • Step 3 : Reassigning heavy chain V gene alleles (optional but recommended)
    • Step 4: Assigning constant region calls
    • Step 5: Quantify mutations (optional).
  • Filtering
  • BCR clustering and visualization
    • Quick primer to the Dandelion class
    • Finding clones
    • Visualization of BCR network
    • Integration with scanpy
    • Calculating mutational load
    • Calculating size of clones
    • Calculating diversity
    • Additional plotting functions
  • Running from R
    • Foreword
    • Pre-processing
    • Filtering
    • Finding clones
    • Calculating size of clones
    • Generate BCR network visualization
    • Integrating with Seurat
    • Plotting BCR network

API:

  • Preprocessing: pp
  • Preprocessing (external): pp.external
  • Tools: tl
  • Plotting: pl
  • Utilities: utl
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