NAIR-package |
NAIR: 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 Receptor Sequences |
buildAssociatedClusterNetwork |
Build Global Network of Associated TCR/BCR Clusters |
buildNet |
Network Analysis of Immune Repertoire |
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 |
exclusiveNodeStats |
Specify Node-level Network Properties to Compute |
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 |
findAssociatedSeqs2 |
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 |
generateNetworkFromAdjacencyMat |
Generate the 'igraph' for a Network Adjacency Matrix |
generateNetworkGraph |
Generate the 'igraph' for a Network Adjacency Matrix |
generateNetworkGraphPlots |
Generate Plots of a Network Graph |
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 |
loadDataFromFileList |
Load and Combine Data From Multiple Samples |
NAIR |
NAIR: Network Analysis of Immune Repertoire |
node_stat_settings |
Specify Node-level Network Properties to Compute |
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 |
sparseAdjacencyMatFromSeqs |
Compute Graph Adjacency Matrix for Immune Repertoire Network |