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