AntibodyForests1.1.0 package

Function to add node features to an AntibodyForests-object

Function to infer B cell evolutionary networks for all clonotypes in V...

Function to make a grouped boxplot of metrics from clusters of clonoty...

Function to create a barplot of the cluster composition of selected fe...

A function to compare dynamics of B cell evolution across different re...

Function to compare trees created with different algorithms from the s...

Function to compare the distributions of the Protein Language Model pr...

Function to compare tree topology of B cell lineages

Function to make a grouped boxplot of distance between nodes from spec...

Function to scatterplot the distance to the germline to a numerical no...

Function to calculate the RMSD between sequences over each edge in the...

Function to get the sequences from the nodes in an AntibodyForest obje...

Function to calculate metrics for each tree in an AntibodyForests-obje...

Function to make a grouped boxplot of the normalized average node size...

Function to create a dataframe of the Protein Language Model probabili...

Function to create a boxplot of the Protein Language Model probabiliti...

Function to create a distribution plot of the Protein Language Model p...

Plots lineage tree of clonotype from AntibodyForests object

Function to synchronize the node labels/names of all clonotypes within...

Saves an AntibodyForests-object into a newick file

Calculate the GBLD distance between trees in an AntibodyForests object...

Converts an igraph network into a phylogenetic tree as a phylo object.

Converts files with phylogenetic trees in newick format into an Antibo...

Function to calculate 3D-structure propoperties such as the average ch...

Function to import the annotations and alignments from IgBLAST output ...

A function to integrate bulk and single cell data

Function to convert VDJ dataframe into an AIRR-formatted TSV file.