Man pages for mlizhangx/Network-Analysis-for-Repertoire-Sequencing-
Network Analysis of Immune Repertoire
| addClusterLabels | Label Clusters in a Network Graph Plot |
| addClusterMembership | Partition a Network Graph Into Clusters |
| addClusterStats | Compute Cluster-Level Network Properties |
| addGraphLabels | Label Nodes in a Network Graph Plot |
| 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... |
| 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... |
| 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... |
| 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... |
| hamDistBounded | Bounded Computation of Hamming Distance |
| levDistBounded | Bounded Computation of Levenshtein Distance |
| NAIR-package | NAIR: Network Analysis of Immune Repertoire |
| 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 |
