Files in ramellose/NetworkUtils
Network analysis utitilities for "From hairballs to hypotheses: biological insights from microbial networks"
.Rbuildignore
.Rhistory
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NetworkUtils.Rproj
R/analyseDeg.R
R/analyseHubs.R
R/analyseKlemm.R
R/analyseOutput.R
R/callTools.R
R/computeAUC.R
R/computeAdjacency.R
R/computeCentral.R
R/computeHub.R
R/computePrecision.R
R/computeSensitivity.R
R/computeSpecificity.R
R/computeStat.R
R/envGrowthChanges.R
R/generateKlemms.R
R/generateSets.R
R/plotHubs.R
R/plotPrecisionvsRecall.R
R/plotSeries.R
R/plotStats.R
R/plotSuperSet.R
R/plotUpset.R
R/readCoNet.R
R/readSpar.R
R/testSpear.R
R/testSpiec.R
R/testgCoda.R
R/writeFeatures.R
R/writeSets.R
README.Rmd
README.md
data/Environmental factor networks/CoNet Brown_env_nofeatures_networks.rds
data/Environmental factor networks/CoNet Brown_env_results.rds
data/Environmental factor networks/CoNet Brown_env_withfeatures_networks.rds
data/Environmental factor networks/CoNet Fisher_env_nofeatures_networks.rds
data/Environmental factor networks/CoNet Fisher_env_results.rds
data/Environmental factor networks/CoNet Fisher_env_withfeatures_networks.rds
data/Environmental factor networks/SPIEC-EASI GL_env_results.rds
data/Environmental factor networks/SPIEC-EASI MB_env_results.rds
data/Environmental factor networks/SparCC _env_networks.rds
data/Environmental factor networks/SparCC_env_results.rds
data/Environmental factor networks/Spearman_env_networks.rds
data/Environmental factor networks/Spearman_env_results.rds
data/Environmental factor networks/SpiecEasi GL_env_networks.rds
data/Environmental factor networks/SpiecEasi MB_env_networks.rds
data/Environmental factor networks/gCoda_env_networks.rds
data/Environmental factor networks/gCoda_env_results.rds
data/Hub species networks/CoNet_brown_hubs_networks.rds
data/Hub species networks/CoNet_fisher_hubs_networks.rds
data/Hub species networks/SparCC_hubs_networks.rds
data/Hub species networks/Spearman_hubs_networks.rds
data/Hub species networks/SpiecEasi GL_hubs_networks.rds
data/Hub species networks/SpiecEasi MB_hubs_networks.rds
data/Hub species networks/gCoda_hubs_networks.rds
data/Modules data/CoNet_brown__env_modules_bashnetworks.rds
data/Modules data/SpiecEasi MB_env_modulesnetworks.rds
data/Modules data/_env_modules.rds
data/Modules data/environmentalfactors+species_edges.rds
data/bashscript_CoNet.bash
data/bashscript_SparCC.bash
data/env_dataset.rds
data/hubklemm_adj.rds
data/hubklemm_interactions.rds
data/hubs_dataset.rds
data/klemm_adj.rds
data/klemm_interactions.rds
data/klemmspecs.rds
docs/LICENSE.html
docs/articles/environmental-factors.R
docs/articles/environmental-factors.html
docs/articles/environmental-factors_files/figure-html/unnamed-chunk-3-1.png
docs/articles/environmental-factors_files/figure-html/unnamed-chunk-3-2.png
docs/articles/hub-species.R
docs/articles/hub-species.html
docs/articles/hub-species_files/figure-html/unnamed-chunk-3-1.png
docs/articles/hub-species_files/figure-html/unnamed-chunk-3-2.png
docs/articles/hub-species_files/figure-html/unnamed-chunk-4-1.png
docs/articles/index.html
docs/articles/testing_network_tools.html
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/reference/analyseDeg.html
docs/reference/analyseHubs.html
docs/reference/analyseKlemm.html
docs/reference/analyseOutput.html
docs/reference/callTools.html
docs/reference/computeAUC.html
docs/reference/computeAdjacency.html
docs/reference/computeCentral.html
docs/reference/computeHub.html
docs/reference/computePrecision.html
docs/reference/computeSensitivity.html
docs/reference/computeSpecificity.html
docs/reference/computeStat.html
docs/reference/envGrowthChanges.html
docs/reference/generateKlemms.html
docs/reference/generateSets.html
docs/reference/index.html
docs/reference/plotHubs.html
docs/reference/plotPrecisionvsRecall.html
docs/reference/plotSeries.html
docs/reference/plotStats.html
docs/reference/plotSuperSet.html
docs/reference/plotUpset.html
docs/reference/readCoNet.html
docs/reference/readSpar.html
docs/reference/testSpear.html
docs/reference/testSpiec.html
docs/reference/testgCoda.html
docs/reference/writeFeatures.html
docs/reference/writeSets.html
man/analyseDeg.Rd
man/analyseHubs.Rd
man/analyseKlemm.Rd
man/analyseOutput.Rd
man/callTools.Rd
man/computeAUC.Rd
man/computeAdjacency.Rd
man/computeCentral.Rd
man/computeHub.Rd
man/computePrecision.Rd
man/computeSensitivity.Rd
man/computeSpecificity.Rd
man/computeStat.Rd
man/envGrowthChanges.Rd
man/generateKlemms.Rd
man/generateSets.Rd
man/plotHubs.Rd
man/plotPrecisionvsRecall.Rd
man/plotSeries.Rd
man/plotStats.Rd
man/plotSuperSet.Rd
man/plotUpset.Rd
man/readCoNet.Rd
man/readSpar.Rd
man/testSpear.Rd
man/testSpiec.Rd
man/testgCoda.Rd
man/writeFeatures.Rd
man/writeSets.Rd
vignettes/environmental-factors.Rmd
vignettes/hub-species.Rmd
vignettes/testing_network_tools.Rmd
