NAIR-package            NAIR: Network Analysis of Immune Repertoire
addClusterMembership    Partition a Network Graph Into Clusters
addClusterStats         Compute Cluster-Level Network Properties
addNodeNetworkStats     Compute Node-Level Network Properties
addNodeStats            Compute Node-Level Network Properties
addPlots                Generate Plots of a Network Graph
aggregateIdenticalClones
                        Aggregate Counts/Frequencies for Clones With
                        Identical Receptor Sequences
buildAssociatedClusterNetwork
                        Build Global Network of Associated TCR/BCR
                        Clusters
buildPublicClusterNetwork
                        Build Global Network of Public TCR/BCR Clusters
buildPublicClusterNetworkByRepresentative
                        Build Global Network of Public TCR/BCR Clusters
                        Using Representative Clones
buildRepSeqNetwork      Network Analysis of Immune Repertoire
chooseNodeStats         Specify Node-level Network Properties to
                        Compute
combineSamples          Load and Combine Data From Multiple Samples
extractLayout           Get Coordinate Layout From Graph Plot
filterInputData         Filter Data Rows and Subset Data Columns
findAssociatedClones    Identify TCR/BCR Clones in a Neighborhood
                        Around Each Associated Sequence
findAssociatedSeqs      Identify TCR/BCR Sequences Associated With a
                        Binary Variable
findPublicClusters      Find Public Clusters Among RepSeq Samples
generateAdjacencyMatrix
                        Compute Graph Adjacency Matrix for Immune
                        Repertoire Network
generateNetworkGraph    Generate the 'igraph' for a Network Adjacency
                        Matrix
generateNetworkObjects
                        Generate Basic Output for an Immune Repertoire
                        Network
getClusterStats         Compute Cluster-Level Network Properties
getNeighborhood         Identify Cells or Clones in a Neighborhood
                        Around a Target Sequence
hamDistBounded          Bounded Computation of Hamming Distance
labelClusters           Label Clusters in a Network Graph Plot
labelNodes              Label Nodes in a Network Graph Plot
levDistBounded          Bounded Computation of Levenshtein Distance
plotNetworkGraph        Plot the Graph of an Immune Repertoire Network
saveNetwork             Save List of Network Objects
saveNetworkPlots        Write Plots to a PDF
simulateToyData         Generate Toy AIRR-Seq Data
