HVGERM                  Human IGHV germlines
alleleClusterNames      Allele similarity cluster naming scheme
allele_cluster_table    Allele similarity cluster table
allele_diff             Alleles nucleotide position difference
allele_diff_indices     Calculate differences between characters in
                        columns of germs and return their indices as an
                        int vector.
allele_diff_indices_parallel
                        Calculate SNPs or their count for each
                        germline-input sequence pair with optional
                        parallel execution.
allele_diff_indices_parallel2
                        Calculate SNPs or their count for each
                        germline-input sequence pair with optional
                        parallel execution.
allele_diff_strings     Calculate differences between characters in
                        columns of germs and return them as a string
                        vector.
allele_threshold_table
                        Allele thresholds table
artificialFRW1Germline
                        FWR1 artificial dataset generator
assignAlleleClusters    Assign allele similarity clusters
detect_communities_leiden
                        Leiden community detection
distance_to_graph       Convert distance matrix to weighted graph
extractASCTable         Extracts the allele cluster table from the
                        archive file.
generateReferenceSet    Generate allele similarity reference set
germlineASC             Converts IGHV germline set to ASC germline set.
hv_functionality        Human IGHV germlines functionality description
igClust                 Allele similarity clustering
igDistance              Germline set alleles distance
ighvClust               Allele similarity clustering (deprecated)
ighvDistance            Germline set alleles distance (deprecated)
inferAlleleClusters     Allele similarity cluster
inferGenotypeAllele     Allele based genotype inference
inferGenotypeAllele_asc
                        Allele similarity cluster based genotype
                        inference Testing function
insert_gaps2_vec        Insert gaps into an ungapped sequence based on
                        a gapped reference sequence.
new_germline_cluster    Create a GermlineCluster object
optimize_resolution     Optimize resolution parameter using silhouette
                        score
piglet                  The Program for Ig clusters (PIgLET) package
plot.GermlineCluster    Plot method for GermlineCluster
plotAlleleCluster       Plotting the dendrogram of the clusters
plotClusterComparison   Compare hierarchical and Leiden clustering
plotCommunityNetwork    Plot community network
plotSilhouetteOptimization
                        Plot silhouette optimization results
plotTruncatedTree       Plot truncated tree visualization
print.GermlineCluster   Print method for GermlineCluster
recentAlleleClusters    Retrieving allele similarity clusters Zenodo
                        archive
summary.GermlineCluster
                        Summary method for GermlineCluster
zenodoArchive           zenodoArchive
