AbForests_AntibodyForest	AbForests_AntibodyForest
AbForests_CompareForests	AbForests_CompareForests
AbForests_ConvertStructure	AbForests_ConvertStructure
AbForests_CsvToDf	AbForests_CsvToDf
AbForests_ForestMetrics	AbForests_ForestMetrics
AbForests_PlotGraphs	AbForests_PlotGraphs
AbForests_PlyloToMatrix	AbForests_PlyloToMatrix
AbForests_RemoveNets	AbForests_RemoveNets
AbForests_SubRepertoiresByCells	AbForests_SubRepertoiresByCells
AbForests_SubRepertoiresByUniqueSeq	AbForests_SubRepertoiresByUniqueSeq
AbForests_UniqueAntibodyVariants	AbForests_UniqueAntibodyVariants
AlphaFold_prediction	AlphaFold_prediction
AntibodyForests	AntibodyForests
AntibodyForests_communities	AntibodyForests_communities
AntibodyForests_dynamics	AntibodyForests_dynamics
AntibodyForests_embeddings	AntibodyForests_embeddings
AntibodyForests_expand_intermediates	AntibodyForests_expand_intermediates
AntibodyForests_heterogeneous	AntibodyForests_heterogeneous
AntibodyForests_infer_ancestral	AntibodyForests_infer_ancestral
AntibodyForests_join_trees	AntibodyForests_join_trees
AntibodyForests_kernels	AntibodyForests_kernels
AntibodyForests_label_propagation	AntibodyForests_label_propagation
AntibodyForests_metrics	AntibodyForests_metrics
AntibodyForests_node_transitions	AntibodyForests_node_transitions
AntibodyForests_overlap	AntibodyForests_overlap
AntibodyForests_paths	AntibodyForests_paths
AntibodyForests_phylo	AntibodyForests_phylo
AntibodyForests_plot	AntibodyForests_plot
AntibodyForests_plot_metrics	AntibodyForests_plot_metrics
automate_GEX	automate_GEX
Bcell_sequences_example_tree	Bcell_sequences_example_tree
Bcell_tree_2	Bcell_tree_2
call_MIXCR	call_MIXCR
CellPhoneDB_analyse	CellPhoneDB_analyse
class_switch_prob_hum	class_switch_prob_hum
class_switch_prob_mus	class_switch_prob_mus
clonofreq	clonofreq
clonofreq.isotype.data	clonofreq.isotype.data
clonofreq.isotype.plot	clonofreq.isotype.plot
clonofreq.trans.data	clonofreq.trans.data
clonofreq.trans.plot	clonofreq.trans.plot
cluster.id.igraph	cluster.id.igraph
colors	colors
dot_plot	dot_plot
Echidna_simulate_repertoire	Echidna_simulate_repertoire
Echidna_vae_generate	Echidna_vae_generate
get.avr.mut.data	get.avr.mut.data
get.avr.mut.plot	get.avr.mut.plot
get.barplot.errorbar	get.barplot.errorbar
get.elbow	get.elbow
get.n.node.data	get.n.node.data
get.n.node.plot	get.n.node.plot
get.seq.distance	get.seq.distance
get.umap	get.umap
get.vgu.matrix	get.vgu.matrix
GEX_clonotype	GEX_clonotype
GEX_cluster_genes	GEX_cluster_genes
GEX_cluster_genes_heatmap	GEX_cluster_genes_heatmap
GEX_cluster_membership	GEX_cluster_membership
GEX_coexpression_coefficient	GEX_coexpression_coefficient
GEX_DEgenes	GEX_DEgenes
GEX_DEgenes_persample	GEX_DEgenes_persample
GEX_dottile_plot	GEX_dottile_plot
GEX_gene_visualization	GEX_gene_visualization
GEX_GOterm	GEX_GOterm
GEX_GSEA	GEX_GSEA
GEX_heatmap	GEX_heatmap
GEX_lineage_trajectories	GEX_lineage_trajectories
GEX_pairwise_DEGs	GEX_pairwise_DEGs
GEX_phenotype	GEX_phenotype
GEX_phenotype_per_clone	GEX_phenotype_per_clone
GEX_projecTILS	GEX_projecTILS
GEX_proportions_barplot	GEX_proportions_barplot
GEX_pseudobulk	GEX_pseudobulk
GEX_pseudotime_trajectory_plot	GEX_pseudotime_trajectory_plot
GEX_scatter_coexpression	GEX_scatter_coexpression
GEX_topN_DE_genes_per_cluster	GEX_topN_DE_genes_per_cluster
GEX_trajectories	GEX_trajectories
GEX_visualize_clones	GEX_visualize_clones
GEX_volcano	GEX_volcano
hotspot_df	hotspot_df
hum_b_h	hum_b_h
hum_b_l	hum_b_l
hum_t_h	hum_t_h
hum_t_l	hum_t_l
iso_SHM_prob	iso_SHM_prob
mus_b_h	mus_b_h
mus_b_l	mus_b_l
mus_b_trans	mus_b_trans
mus_t_h	mus_t_h
mus_t_l	mus_t_l
no.empty.node	no.empty.node
one_spot_df	one_spot_df
pheno_SHM_prob	pheno_SHM_prob
PlatypusDB_AIRR_to_VGM	PlatypusDB_AIRR_to_VGM
PlatypusDB_fetch	PlatypusDB_fetch
PlatypusDB_find_CDR3s	PlatypusDB_find_CDR3s
PlatypusDB_list_projects	PlatypusDB_list_projects
PlatypusDB_load_from_disk	PlatypusDB_load_from_disk
PlatypusDB_VGM_to_AIRR	PlatypusDB_VGM_to_AIRR
PlatypusML_balance	PlatypusML_balance
PlatypusML_classification	PlatypusML_classification
PlatypusML_feature_extraction_GEX	PlatypusML_feature_extraction_GEX
PlatypusML_feature_extraction_VDJ	PlatypusML_feature_extraction_VDJ
select.top.clone	select.top.clone
small_vgm	small_vgm
Spatial_celltype_plot	Spatial_celltype_plot
Spatial_cluster	Spatial_cluster
Spatial_density_plot	Spatial_density_plot
Spatial_evolution_of_clonotype_plot	Spatial_evolution_of_clonotype_plot
Spatial_marker_expression	Spatial_marker_expression
Spatial_module_expression	Spatial_module_expression
Spatial_nb_SHM_compare_to_germline_plot	Spatial_nb_SHM_compare_to_germline_plot
Spatial_scaling_parameters	Spatial_scaling_parameters
Spatial_selection_expanded_clonotypes	Spatial_selection_expanded_clonotypes
Spatial_selection_of_cells_on_image	Spatial_selection_of_cells_on_image
Spatial_VDJ_assignment	Spatial_VDJ_assignment
Spatial_VDJ_plot	Spatial_VDJ_plot
Spatial_vgm_formation	Spatial_vgm_formation
special_v	special_v
trans_switch_prob_b	trans_switch_prob_b
trans_switch_prob_t	trans_switch_prob_t
umap.top.highlight	umap.top.highlight
VDJ_abundances	VDJ_abundances
VDJ_alpha_beta_Vgene_circos	VDJ_alpha_beta_Vgene_circos
VDJ_analyze	VDJ_analyze
VDJ_antigen_integrate	VDJ_antigen_integrate
VDJ_assemble_for_PnP	VDJ_assemble_for_PnP
VDJ_bulk_to_vgm	VDJ_bulk_to_vgm
VDJ_call_enclone	VDJ_call_enclone
VDJ_call_MIXCR	VDJ_call_MIXCR
VDJ_call_MIXCR_full	VDJ_call_MIXCR_full
VDJ_call_RECON	VDJ_call_RECON
VDJ_circos	VDJ_circos
VDJ_clonal_donut	VDJ_clonal_donut
VDJ_clonal_expansion	VDJ_clonal_expansion
VDJ_clonal_expansion_abundances	VDJ_clonal_expansion_abundances
VDJ_clonal_lineages	VDJ_clonal_lineages
VDJ_clonotype	VDJ_clonotype
VDJ_contigs_to_vgm	VDJ_contigs_to_vgm
VDJ_db_annotate	VDJ_db_annotate
VDJ_db_load	VDJ_db_load
VDJ_diversity	VDJ_diversity
VDJ_dublets	VDJ_dublets
VDJ_dynamics	VDJ_dynamics
VDJ_enclone	VDJ_enclone
VDJ_expand_aberrants	VDJ_expand_aberrants
VDJ_extract_germline	VDJ_extract_germline
VDJ_get_public	VDJ_get_public
VDJ_GEX_clonal_lineage_clusters	VDJ_GEX_clonal_lineage_clusters
VDJ_GEX_clonotyme	VDJ_GEX_clonotyme
VDJ_GEX_clonotype_clusters_circos	VDJ_GEX_clonotype_clusters_circos
VDJ_GEX_expansion	VDJ_GEX_expansion
VDJ_GEX_integrate	VDJ_GEX_integrate
VDJ_GEX_matrix	VDJ_GEX_matrix
VDJ_GEX_overlay_clones	VDJ_GEX_overlay_clones
VDJ_GEX_stats	VDJ_GEX_stats
VDJ_isotypes_per_clone	VDJ_isotypes_per_clone
VDJ_kmers	VDJ_kmers
vdj_length_prob	vdj_length_prob
VDJ_logoplot_vector	VDJ_logoplot_vector
VDJ_network	VDJ_network
VDJ_ordination	VDJ_ordination
VDJ_overlap_heatmap	VDJ_overlap_heatmap
VDJ_per_clone	VDJ_per_clone
VDJ_phylogenetic_trees	VDJ_phylogenetic_trees
VDJ_phylogenetic_trees_plot	VDJ_phylogenetic_trees_plot
VDJ_plot_SHM	VDJ_plot_SHM
VDJ_public	VDJ_public
VDJ_rarefaction	VDJ_rarefaction
VDJ_reclonotype_list_arrange	VDJ_reclonotype_list_arrange
VDJ_select_clonotypes	VDJ_select_clonotypes
VDJ_structure_analysis	VDJ_structure_analysis
VDJ_tree	VDJ_tree
VDJ_variants_per_clone	VDJ_variants_per_clone
VDJ_Vgene_usage	VDJ_Vgene_usage
VDJ_Vgene_usage_barplot	VDJ_Vgene_usage_barplot
VDJ_Vgene_usage_stacked_barplot	VDJ_Vgene_usage_stacked_barplot
VDJ_VJ_usage_circos	VDJ_VJ_usage_circos
VGM_expanded_clones	VGM_expanded_clones
VGM_expand_featurebarcodes	VGM_expand_featurebarcodes
VGM_integrate	VGM_integrate
