Package: NAIR 1.0.4.9001

Brian Neal

NAIR: Network Analysis of Immune Repertoire

Pipelines for studying the adaptive immune repertoire of T cells and B cells via network analysis based on receptor sequence similarity. Relate clinical outcomes to immune repertoires based on their network properties, or to particular clusters and clones within a repertoire. Yang et al. (2023) <doi:10.3389/fimmu.2023.1181825>.

Authors:Brian Neal [aut, cre], Hai Yang [aut], Daniil Matveev [aut], Phi Long Le [aut], Li Zhang [cph, aut]

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NAIR.pdf |NAIR.html✨
NAIR/json (API)
NEWS

# Install 'NAIR' in R:
install.packages('NAIR', repos = c('https://mlizhangx.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mlizhangx/network-analysis-for-repertoire-sequencing-/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

40 exports 7 stars 2.01 score 53 dependencies 27 scripts 186 downloads

Last updated 6 months agofrom:ea4bfebca5. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 02 2024
R-4.5-win-x86_64OKSep 02 2024
R-4.5-linux-x86_64OKSep 02 2024
R-4.4-win-x86_64OKSep 02 2024
R-4.4-mac-x86_64OKSep 02 2024
R-4.4-mac-aarch64OKSep 02 2024
R-4.3-win-x86_64OKSep 02 2024
R-4.3-mac-x86_64OKSep 02 2024
R-4.3-mac-aarch64OKSep 02 2024

Exports:addClusterLabelsaddClusterMembershipaddClusterStatsaddGraphLabelsaddNodeNetworkStatsaddNodeStatsaddPlotsaggregateIdenticalClonesbuildAssociatedClusterNetworkbuildNetbuildPublicClusterNetworkbuildPublicClusterNetworkByRepresentativebuildRepSeqNetworkchooseNodeStatscombineSamplesexclusiveNodeStatsextractLayoutfilterInputDatafindAssociatedClonesfindAssociatedSeqsfindAssociatedSeqs2findPublicClustersgenerateAdjacencyMatrixgenerateNetworkFromAdjacencyMatgenerateNetworkGraphgenerateNetworkGraphPlotsgenerateNetworkObjectsgetClusterStatsgetNeighborhoodhamDistBoundedlabelClusterslabelNodeslevDistBoundedloadDataFromFileListnode_stat_settingsplotNetworkGraphsaveNetworksaveNetworkPlotssimulateToyDatasparseAdjacencyMatFromSeqs

Dependencies:cachemclicolorspacecpp11dplyrfansifarverfastmapgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr

buildRepSeqNetwork()/buildNet()

Rendered frombuildRepSeqNetwork.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-09-14
Started: 2022-11-26

Cluster Analysis

Rendered fromcluster_analysis.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-04-05
Started: 2023-09-13

Dual-Chain Network Analysis

Rendered fromdual_chain.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-09-13
Started: 2023-02-21

Introduction to the NAIR package

Rendered fromNAIR.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-09-26
Started: 2022-10-13

Node-Level Network Properties

Rendered fromnode_properties.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-09-13
Started: 2023-09-13

Supplementary Functions

Rendered fromsupplementary.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-09-14
Started: 2023-09-13

Readme and manuals

Help Manual

Help pageTopics
NAIR: Network Analysis of Immune RepertoireNAIR-package NAIR
Partition a Network Graph Into ClustersaddClusterMembership
Compute Cluster-Level Network PropertiesaddClusterStats
Compute Node-Level Network PropertiesaddNodeNetworkStats
Compute Node-Level Network PropertiesaddNodeStats
Generate Plots of a Network GraphaddPlots generateNetworkGraphPlots
Aggregate Counts/Frequencies for Clones With Identical Receptor SequencesaggregateIdenticalClones
Build Global Network of Associated TCR/BCR ClustersbuildAssociatedClusterNetwork
Build Global Network of Public TCR/BCR ClustersbuildPublicClusterNetwork
Build Global Network of Public TCR/BCR Clusters Using Representative ClonesbuildPublicClusterNetworkByRepresentative
Network Analysis of Immune RepertoirebuildNet buildRepSeqNetwork
Specify Node-level Network Properties to ComputechooseNodeStats exclusiveNodeStats node_stat_settings
Load and Combine Data From Multiple SamplescombineSamples loadDataFromFileList
Get Coordinate Layout From Graph PlotextractLayout
Filter Data Rows and Subset Data ColumnsfilterInputData
Identify TCR/BCR Clones in a Neighborhood Around Each Associated SequencefindAssociatedClones
Identify TCR/BCR Sequences Associated With a Binary VariablefindAssociatedSeqs findAssociatedSeqs2
Find Public Clusters Among RepSeq SamplesfindPublicClusters
Compute Graph Adjacency Matrix for Immune Repertoire NetworkgenerateAdjacencyMatrix sparseAdjacencyMatFromSeqs
Generate the 'igraph' for a Network Adjacency MatrixgenerateNetworkFromAdjacencyMat generateNetworkGraph
Generate Basic Output for an Immune Repertoire NetworkgenerateNetworkObjects
Compute Cluster-Level Network PropertiesgetClusterStats
Identify Cells or Clones in a Neighborhood Around a Target SequencegetNeighborhood
Bounded Computation of Hamming DistancehamDistBounded
Label Clusters in a Network Graph PlotaddClusterLabels labelClusters
Label Nodes in a Network Graph PlotaddGraphLabels labelNodes
Bounded Computation of Levenshtein DistancelevDistBounded
Plot the Graph of an Immune Repertoire NetworkplotNetworkGraph
Save List of Network ObjectssaveNetwork
Write Plots to a PDFsaveNetworkPlots
Generate Toy AIRR-Seq DatasimulateToyData