Files in mlizhangx/Network-Analysis-for-Repertoire-Sequencing-
Network Analysis of Immune Repertoire
.Rbuildignore
.github/.gitignore
.github/workflows/check-no-suggests.yaml
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
Network-Analysis-for-Repertoire-Sequencing.Rproj
R/RcppExports.R
R/aaa.R
R/argchecks_lower.R
R/argchecks_mid.R
R/arghecks_upper.R
R/associated_clusters.R
R/main_function.R
R/network_analysis.R
R/public_clusters.R
R/sim_toy_data.R
R/utils.R
R/visualization.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
man/NAIR-package.Rd
man/addClusterLabels.Rd
man/addClusterMembership.Rd
man/addClusterStats.Rd
man/addGraphLabels.Rd
man/addNodeNetworkStats.Rd
man/addNodeStats.Rd
man/addPlots.Rd
man/aggregateIdenticalClones.Rd
man/buildAssociatedClusterNetwork.Rd
man/buildPublicClusterNetwork.Rd
man/buildPublicClusterNetworkByRepresentative.Rd
man/buildRepSeqNetwork.Rd
man/chooseNodeStats.Rd
man/combineSamples.Rd
man/extractLayout.Rd
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/filterInputData.Rd
man/findAssociatedClones.Rd
man/findAssociatedSeqs.Rd
man/findPublicClusters.Rd
man/generateAdjacencyMatrix.Rd
man/generateNetworkGraph.Rd
man/generateNetworkObjects.Rd
man/getClusterStats.Rd
man/getNeighborhood.Rd
man/hamDistBounded.Rd
man/levDistBounded.Rd
man/plotNetworkGraph.Rd
man/saveNetwork.Rd
man/saveNetworkPlots.Rd
man/simulateToyData.Rd
src/Makevars
src/Makevars.win
src/NAIR.dll
src/RcppExports.cpp
src/RcppExports.o
src/dropDegreeZero.cpp
src/dropDegreeZero.h
src/dropDegreeZero.o
src/hamAdjacencyMatSparse.cpp
src/hamAdjacencyMatSparse.o
src/hamDistBounded.cpp
src/hamDistBounded.h
src/hamDistBounded.o
src/levAdjacencyMatSparse.cpp
src/levAdjacencyMatSparse.o
src/levDistBounded.cpp
src/levDistBounded.h
src/levDistBounded.o
src/patternAdjacencyMatSparse.cpp
src/patternAdjacencyMatSparse.o
src/sortAdjacencyMatSparse.cpp
src/sortAdjacencyMatSparse.o
tests/testthat.R
tests/testthat/test_argchecks.R
tests/testthat/test_functions.R
vignettes/NAIR.Rmd
vignettes/associated_clusters.Rmd
vignettes/buildRepSeqNetwork.Rmd
vignettes/cluster_analysis.Rmd
vignettes/dual_chain.Rmd
vignettes/network_visualization.Rmd
vignettes/node_properties.Rmd
vignettes/public_clusters.Rmd
vignettes/supplementary.Rmd
