Files in ravinpoudel/PhONA
PhONA provides a framework to select a testable and manageable number of OTUs/ASVs to support microbiome-based agriculture
.DS_Store
.RData
.Rbuildignore
.Rhistory
.gitignore
DESCRIPTION
NAMESPACE
PhONA.Rproj
R/.DS_Store
R/PhONA.R
R/getMean.R
R/lasso.R
R/model.lasso.R
R/model.linear.R
R/noderoles.R
R/read.mothur.shared.R
R/read.mothur.taxonomy.R
R/removerare.R
R/rolePlot.R
R/summarizePhONA.R
R/taxacolor.R
README.md
ThingsToAdd.R
_pkgdown.yml
docs/.DS_Store
docs/404.html
docs/articles/PhONA-manuscript.html
docs/articles/PhONA-manuscript_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/PhONA-manuscript_files/figure-html/pressure-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-1-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-10-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-11-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-12-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-13-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-15-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-16-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-17-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-18-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-2-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-3-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-4-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-5-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-6-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-7-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-8-1.png
docs/articles/PhONA-manuscript_files/figure-html/unnamed-chunk-9-1.png
docs/articles/PhONA.html
docs/articles/PhONA_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/PhONA_files/figure-html/unnamed-chunk-3-1.png
docs/articles/PhONA_files/figure-html/unnamed-chunk-4-1.png
docs/articles/PhONA_files/figure-html/unnamed-chunk-5-1.png
docs/articles/PhONA_files/figure-html/unnamed-chunk-6-1.png
docs/articles/PhONA_files/figure-html/unnamed-chunk-7-1.png
docs/articles/PhONA_files/figure-html/unnamed-chunk-9-1.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/figures/PhONA.png
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/PhONA.html
docs/reference/Rplot001.png
docs/reference/getMean.html
docs/reference/index.html
docs/reference/kmeans_cluster.html
docs/reference/lasso.html
docs/reference/model.lasso.html
docs/reference/model.linear.html
docs/reference/node.role.html
docs/reference/read.mothur.shared.html
docs/reference/read.mothur.taxonomy.html
docs/reference/remove_rare.html
docs/reference/rolePlot.html
docs/reference/summarizePhONA.html
docs/reference/summary.graph.html
docs/reference/taxacolor.html
figures/PhONA.png
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/cor_sparcc.out
inst/extdata/physeqobject.rds
inst/extdata/pvals.txt
man/PhONA.Rd
man/getMean.Rd
man/lasso.Rd
man/model.lasso.Rd
man/model.linear.Rd
man/node.role.Rd
man/read.mothur.shared.Rd
man/read.mothur.taxonomy.Rd
man/remove_rare.Rd
man/rolePlot.Rd
man/summarizePhONA.Rd
man/taxacolor.Rd
ms_code.R
ms_run/.DS_Store
ms_run/data/.DS_Store
ms_run/data/2015Fungi-RhizosphereFinal.oligos
ms_run/data/2015Fungi-RootFinal.oligos
ms_run/data/Fungi1415_Metadata.xlsx
ms_run/data/Fungi1415_trim.contigs.trim.unique.precluster.pick.pick.subsample.nn.unique_list.0.03.cons.tax.summary
ms_run/data/Fungi1415_trim.contigs.trim.unique.precluster.pick.pick.subsample.nn.unique_list.0.03.cons.taxonomy
ms_run/data/Fungi1415_trim.contigs.trim.unique.precluster.pick.pick.subsample.nn.unique_list.count.summary
ms_run/data/Fungi1415_trim.contigs.trim.unique.precluster.pick.pick.subsample.nn.unique_list.shared
ms_run/data/block_diversity_selected_tunnel_ww.csv
ms_run/data/cleaned.count_table
ms_run/data/figures/.DS_Store
ms_run/data/figures/.Rmd
ms_run/data/figures/phona_maxi_endo.pdf
ms_run/data/figures/phona_maxi_rhizo.pdf
ms_run/data/figures/phona_ng_endo.pdf
ms_run/data/figures/phona_ng_rhizo.pdf
ms_run/data/figures/phona_rst_endo.pdf
ms_run/data/figures/phona_rst_rhizo.pdf
ms_run/data/figures/phona_sg_end.pdf
ms_run/data/figures/phona_sg_rhizo.pdf
ms_run/data/figures/roles_endo.pdf
ms_run/data/figures/roles_rhizo.pdf
ms_run/data/figures/summary_graph_endo.csv
ms_run/data/figures/summary_graph_rhizo.csv
ms_run/data/name.png
ms_run/data/role_df_Endosphere.csv
ms_run/data/role_df_Rhizosphere.csv
ms_run/data/role_df_all.csv
ms_run/data/sparcc_data/maxi_endo_sparcc.txt
ms_run/data/sparcc_data/maxi_rhizo_sparcc.txt
ms_run/data/sparcc_data/ng_endo_sparcc.txt
ms_run/data/sparcc_data/ng_rhizo_sparcc.txt
ms_run/data/sparcc_data/rst_endo_sparcc.txt
ms_run/data/sparcc_data/rst_rhizo_sparcc.txt
ms_run/data/sparcc_data/sg_endo_sparcc.txt
ms_run/data/sparcc_data/sg_rhizo_sparcc.txt
ms_run/data/sparcc_output/.DS_Store
ms_run/data/sparcc_output/Endosphere_Maxifort.txt
ms_run/data/sparcc_output/Endosphere_Maxifort_cor_sparcc.out
ms_run/data/sparcc_output/Endosphere_Maxifort_pvals.two_sided-new.txt
ms_run/data/sparcc_output/Endosphere_Maxifort_pvals.two_sided.txt
ms_run/data/sparcc_output/Endosphere_Nongraft.txt
ms_run/data/sparcc_output/Endosphere_Nongraft_cor_sparcc.out
ms_run/data/sparcc_output/Endosphere_Nongraft_pvals.two_sided.txt
ms_run/data/sparcc_output/Endosphere_RST-04-106.txt
ms_run/data/sparcc_output/Endosphere_RST-04-106_cor_sparcc.out
ms_run/data/sparcc_output/Endosphere_RST-04-106_pvals.two_sided.txt
ms_run/data/sparcc_output/Endosphere_Selfgraft.txt
ms_run/data/sparcc_output/Endosphere_Selfgraft_cor_sparcc.out
ms_run/data/sparcc_output/Endosphere_Selfgraft_pvals.two_sided.txt
ms_run/data/sparcc_output/Rhizosphere_Maxifort.txt
ms_run/data/sparcc_output/Rhizosphere_Maxifort_cor_sparcc.out
ms_run/data/sparcc_output/Rhizosphere_Maxifort_pvals.two_sided.txt
ms_run/data/sparcc_output/Rhizosphere_Nongraft.txt
ms_run/data/sparcc_output/Rhizosphere_Nongraft_cor_sparcc.out
ms_run/data/sparcc_output/Rhizosphere_Nongraft_pvals.two_sided.txt
ms_run/data/sparcc_output/Rhizosphere_RST-04-106.txt
ms_run/data/sparcc_output/Rhizosphere_RST-04-106_cor_sparcc.out
ms_run/data/sparcc_output/Rhizosphere_RST-04-106_pvals.two_sided.txt
ms_run/data/sparcc_output/Rhizosphere_SelfGraft.txt
ms_run/data/sparcc_output/Rhizosphere_Selfgraft_cor_sparcc.out
ms_run/data/sparcc_output/Rhizosphere_Selfgraft_pvals.two_sided.txt
ms_run/data/tao_df_sel.csv
ms_run/data/tomato_yield.csv
ms_run/figures_100/.DS_Store
ms_run/figures_100/phona_maxi_endo.pdf
ms_run/figures_100/phona_maxi_rhizo.pdf
ms_run/figures_100/phona_ng_endo.pdf
ms_run/figures_100/phona_ng_rhizo.pdf
ms_run/figures_100/phona_rst_endo.pdf
ms_run/figures_100/phona_rst_rhizo.pdf
ms_run/figures_100/phona_sg_end.pdf
ms_run/figures_100/phona_sg_rhizo.pdf
ms_run/figures_100/roles_endo.pdf
ms_run/figures_500/.DS_Store
ms_run/figures_500/.RData
ms_run/figures_500/.Rhistory
ms_run/figures_500/ms_code.R
ms_run/figures_500/phona_maxi_endo.pdf
ms_run/figures_500/phona_maxi_rhizo.pdf
ms_run/figures_500/phona_ms_run.RData
ms_run/figures_500/phona_ng_endo.pdf
ms_run/figures_500/phona_ng_rhizo.pdf
ms_run/figures_500/phona_rst_endo.pdf
ms_run/figures_500/phona_rst_rhizo.pdf
ms_run/figures_500/phona_sg_end.pdf
ms_run/figures_500/phona_sg_rhizo.pdf
ms_run/figures_500/roles_endo.pdf
ms_run/figures_500/roles_rhizo.pdf
ms_run/figures_500/summary_graph_endo.csv
ms_run/figures_500/summary_graph_rhizo.csv
phona_ms_run.RData
run.R
test.csv
vignettes/.DS_Store
vignettes/.RData
vignettes/.Rhistory
vignettes/PhONA-manuscript.Rmd
vignettes/PhONA.Rmd
vignettes/PhONA.log
vignettes/PhONA.md
vignettes/PhONA.webarchive
vignettes/PhONA_files/.DS_Store
vignettes/PhONA_files/figure-markdown_strict/unnamed-chunk-2-1.png
vignettes/PhONA_files/figure-markdown_strict/unnamed-chunk-3-1.png
vignettes/ms_code.R
