BLOSUM62 |
BLOSUM62 matrix |
CDR3ab |
Mock data set of complementarity determining region 3 (CDR3) sequences and variable (V) and joining (J) genes from the alpha and beta chains of 10,000 T cell receptors. |
class:clust_irr |
clust_irr class |
cluster_irr |
Clustering of immune receptor repertoires (IRRs) |
clust_irr |
clust_irr class |
clust_irr-class |
clust_irr class |
dco |
Model-based differential community occupancy (DCO) analysis |
detect_communities |
Graph-based community detection (GCD) |
get_ag_summary |
Estimate the number of antigen-specific T-cells in selected communities |
get_beta_violins |
Generate beta violin plot: visualize distribution of beta coefficient means for communities in immune receptor repertoires |
get_clustirr_clust |
clust_irr class |
get_clustirr_clust-method |
clust_irr class |
get_clustirr_inputs |
clust_irr class |
get_clustirr_inputs-method |
clust_irr class |
get_graph |
Get 'igraph' object from 'clust_irr' object |
get_honeycombs |
Generate honycomb plot: visualize community occupancy of pairs of immune receptor repertoires |
get_joint_graph |
Create joint 'igraph' object from multiple 'clust_irr' objects |
mcpas |
CDR3 sequences and their matching epitopes obtained from McPAS-TCR |
plot_graph |
Plot ClustIRR graph |
tcr3d |
CDR3 sequences and their matching epitopes obtained from TCR3d |
vdjdb |
CDR3 sequences and their matching epitopes obtained from VDJdb |