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>.

Version: 1.0.4
Depends: R (≥ 3.1.0)
Imports: Rcpp (≥ 1.0.8), lifecycle, igraph, ggraph, ggplot2, grDevices, utils, Matrix, stats, dplyr, rlang
LinkingTo: Rcpp, RcppArmadillo (≥ 0.10.8.0.0)
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2024-03-03
Author: Brian Neal [aut, cre], Hai Yang [aut], Daniil Matveev [aut], Phi Long Le [aut], Li Zhang [cph, aut]
Maintainer: Brian Neal <Brian.Neal at ucsf.edu>
License: GPL (≥ 3)
URL: https://mlizhangx.github.io/Network-Analysis-for-Repertoire-Sequencing-/, https://github.com/mlizhangx/Network-Analysis-for-Repertoire-Sequencing-
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: NAIR results

Documentation:

Reference manual: NAIR.pdf
Vignettes: Introduction to the NAIR package
buildRepSeqNetwork()/buildNet()
Cluster Analysis
Dual-Chain Network Analysis
Node-Level Network Properties
Supplementary Functions

Downloads:

Package source: NAIR_1.0.4.tar.gz
Windows binaries: r-prerel: NAIR_1.0.4.zip, r-release: NAIR_1.0.4.zip, r-oldrel: NAIR_1.0.4.zip
macOS binaries: r-prerel (arm64): NAIR_1.0.4.tgz, r-release (arm64): NAIR_1.0.4.tgz, r-oldrel (arm64): NAIR_1.0.4.tgz, r-prerel (x86_64): NAIR_1.0.4.tgz, r-release (x86_64): NAIR_1.0.4.tgz
Old sources: NAIR archive

Linking:

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