WASP

WASP: A Workflow for Antibody Sequencing Profiling of Single-cell Immune Repertoire Data

The notebooks use functions and documentation from Immcantation, publications linked under Method

Task	Method	Notebook
1. Annotate V(D)J genes	ChangeO
2. Discover novel alleles and correct annotations	TIgGER
3. Infer clonal relationships	SCOPer
4. Reconstruct germlines and trees	Dowser

Name		Name	Last commit message	Last commit date
Latest commit History 60 Commits
Immcantation_1_VDJ_Annotation_and_Standardization_with_Change_O_in_Python.ipynb		Immcantation_1_VDJ_Annotation_and_Standardization_with_Change_O_in_Python.ipynb
Immcantation_2_Novel_V_gene_alleles_with_TIgGER_in_R.ipynb		Immcantation_2_Novel_V_gene_alleles_with_TIgGER_in_R.ipynb
Immcantation_3_Clonal_relationship_inference_with_SHazaM_and_SCOPer_in_R.ipynb		Immcantation_3_Clonal_relationship_inference_with_SHazaM_and_SCOPer_in_R.ipynb
Immcantation_4_Reconstruct_germlines_with_Dowser_in_R.ipynb		Immcantation_4_Reconstruct_germlines_with_Dowser_in_R.ipynb
Immcantation_4_Reconstruct_germlines_with_Dowser_in_R_v2.ipynb		Immcantation_4_Reconstruct_germlines_with_Dowser_in_R_v2.ipynb
Immcantation_clonal_diversity_mutation_analysis.ipynb		Immcantation_clonal_diversity_mutation_analysis.ipynb
README.md		README.md

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