Man pages for AntibodyForests
Delineating Inter- And Intra-Antibody Repertoire Evolution
| Af_add_node_feature | Function to add node features to an AntibodyForests-object |
| Af_build | Function to infer B cell evolutionary networks for all... |
| Af_cluster_metrics | Function to make a grouped boxplot of metrics from clusters... |
| Af_cluster_node_features | Function to create a barplot of the cluster composition of... |
| Af_compare_across_repertoires | A function to compare dynamics of B cell evolution across... |
| Af_compare_methods | Function to compare trees created with different algorithms... |
| Af_compare_PLM | Function to compare the distributions of the Protein Language... |
| Af_compare_within_repertoires | Function to compare tree topology of B cell lineages |
| af_default | Small AntibodyForests object with default algorithm for... |
| Af_distance_boxplot | Function to make a grouped boxplot of distance between nodes... |
| Af_distance_scatterplot | Function to scatterplot the distance to the germline to a... |
| Af_edge_RMSD | Function to calculate the RMSD between sequences over each... |
| Af_get_sequences | Function to get the sequences from the nodes in an... |
| Af_metrics | Function to calculate metrics for each tree in an... |
| af_mst | Small AntibodyForests object with MST algorithm for function... |
| af_nj | Small AntibodyForests object with NJ algorithm for function... |
| Af_node_size_boxplot | Function to make a grouped boxplot of the normalized average... |
| Af_PLM_dataframe | Function to create a dataframe of the Protein Language Model... |
| Af_plot_PLM | Function to create a distribution plot of the Protein... |
| Af_plot_PLM_mut_vs_cons | Function to create a boxplot of the Protein Language Model... |
| Af_plot_tree | Plots lineage tree of clonotype from AntibodyForests object |
| Af_sync_nodes | Function to synchronize the node labels/names of all... |
| Af_to_newick | Saves an AntibodyForests-object into a newick file |
| calculate_GBLD | Calculate the GBLD distance between trees in an... |
| compare_repertoire | Example output from Af_compare_within_repertoires() for... |
| igraph_to_phylo | Converts an igraph network into a phylogenetic tree as a... |
| newick_to_Af | Converts files with phylogenetic trees in newick format into... |
| PLM_dataframe | Small PLM dataframe for function testing purposes |
| small_af | Small AntibodyForests object for function testing purposes |
| small_vdj | Small VDJ dataframe for function testing purposes |
| VDJ_3d_properties | Function to calculate 3D-structure propoperties such as the... |
| VDJ_import_IgBLAST_annotations | Function to import the annotations and alignments from... |
| VDJ_integrate_bulk | A function to integrate bulk and single cell data |
| VDJ_to_AIRR | Function to convert VDJ dataframe into an AIRR-formatted TSV... |
