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scRepertoire
2.7.2
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Vignettes
Getting Set Up
Installation Instructions
Loading Data into scRepertoire
Combining Contigs into Clones
Additional Processing Steps
Repertoire Analysis
Basic Clonal Visualizations
Visualizing Clonal Dynamics
Summarizing Repertoires
Comparing Clonal Diversity and Overlap
Clustering by Edit Distance
Working with Single-Cell Objects
Combining Clones and Single-Cell Objects
Visualizations for Single-Cell Objects
Quantifying Clonal Bias
Extensions
Related Packages
Making Deep Learning Models with immApex
Combining Deep Learning and TCRs with Trex
Combining Deep Learning and BCRs with Ibex
Bridging Python TCR Tools with immLynx
TCR Specificity Grouping with immGLIPH
Immune Reference Data with immReferent
Single-cell Gene Set Enrichment with escape
Compatible Packages
Third-Party Integrations
Combining Immcantation and scRepertoire
TCRpheno Applied to T Cell Fate
Downstream Analysis with immunarch
VDJ Trajectory Analysis with dandelionR
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