Package: NAIR 1.0.4
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:
NAIR_1.0.4.tar.gz
NAIR_1.0.4.tar.gz(r-4.5-noble)NAIR_1.0.4.tar.gz(r-4.4-noble)
NAIR_1.0.4.tgz(r-4.4-emscripten)NAIR_1.0.4.tgz(r-4.3-emscripten)
NAIR.pdf |NAIR.html✨
NAIR/json (API)
NEWS
# Install 'NAIR' in R: |
install.packages('NAIR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mlizhangx/network-analysis-for-repertoire-sequencing-/issues
Pkgdown:https://mlizhangx.github.io
Last updated 9 months agofrom:64e5f129c5. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 28 2024 |
R-4.5-linux-x86_64 | OK | Nov 28 2024 |
Exports:addClusterLabelsaddClusterMembershipaddClusterStatsaddGraphLabelsaddNodeNetworkStatsaddNodeStatsaddPlotsaggregateIdenticalClonesbuildAssociatedClusterNetworkbuildNetbuildPublicClusterNetworkbuildPublicClusterNetworkByRepresentativebuildRepSeqNetworkchooseNodeStatscombineSamplesexclusiveNodeStatsextractLayoutfilterInputDatafindAssociatedClonesfindAssociatedSeqsfindAssociatedSeqs2findPublicClustersgenerateAdjacencyMatrixgenerateNetworkFromAdjacencyMatgenerateNetworkGraphgenerateNetworkGraphPlotsgenerateNetworkObjectsgetClusterStatsgetNeighborhoodhamDistBoundedlabelClusterslabelNodeslevDistBoundedloadDataFromFileListnode_stat_settingsplotNetworkGraphsaveNetworksaveNetworkPlotssimulateToyDatasparseAdjacencyMatFromSeqs
Dependencies:cachemclicolorspacecpp11dplyrfansifarverfastmapgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr
buildRepSeqNetwork()/buildNet()
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usingknitr::rmarkdown
on Nov 28 2024.Last update: 2023-09-14
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Cluster Analysis
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Dual-Chain Network Analysis
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Introduction to the NAIR package
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usingknitr::rmarkdown
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Node-Level Network Properties
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Supplementary Functions
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on Nov 28 2024.Last update: 2023-09-14
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