├── .Rbuildignore ├── .github └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── pr-commands.yaml ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── ReporterScore-package.R ├── calculation.R ├── check_files.R ├── data.R ├── enrichment.R ├── kegg_net.R ├── plot.R ├── print.R └── utils-pipe.R ├── README.Rmd ├── README.md ├── README_zh_CN.md ├── _pkgdown.yml ├── data ├── CPDlist.rda ├── Compound_htable.rda ├── KO_abundance_test.rda ├── KO_htable.rda ├── KOlist.rda ├── Module_htable.rda ├── Pathway_htable.rda ├── genedf.rda ├── hsa_kegg_pathway.rda ├── mmu_kegg_pathway.rda └── reporter_score_res.rda ├── inst └── CITATION ├── man ├── CPDlist.Rd ├── Compound_htable.Rd ├── GOlist.Rd ├── KO_abundance.Rd ├── KO_enrich.Rd ├── KO_fisher.Rd ├── KO_gsa.Rd ├── KO_gsea.Rd ├── KO_gsva.Rd ├── KO_htable.Rd ├── KO_padog.Rd ├── KO_safe.Rd ├── KO_sea.Rd ├── KOlist.Rd ├── Module_htable.Rd ├── Pathway_htable.Rd ├── RSA_by_cm.Rd ├── ReporterScore-package.Rd ├── c_means.Rd ├── c_net_from_pathway_xml.Rd ├── calculate_NS.Rd ├── calculate_ZN_score.Rd ├── combine_rs_res.Rd ├── custom_modulelist.Rd ├── custom_modulelist_from_org.Rd ├── export_report_table.Rd ├── figures │ ├── 1-workflow.png │ ├── README-unnamed-chunk-10-1.png │ ├── README-unnamed-chunk-11-1.png │ ├── README-unnamed-chunk-12-1.png │ ├── README-unnamed-chunk-13-1.png │ ├── README-unnamed-chunk-14-1.png │ ├── README-unnamed-chunk-15-1.png │ ├── README-unnamed-chunk-16-1.png │ ├── README-unnamed-chunk-17-1.png │ ├── README-unnamed-chunk-18-1.png │ ├── README-unnamed-chunk-19-1.png │ ├── README-unnamed-chunk-19-2.png │ ├── README-unnamed-chunk-20-1.png │ ├── README-unnamed-chunk-20-2.png │ ├── README-unnamed-chunk-21-1.png │ ├── README-unnamed-chunk-21-2.png │ ├── README-unnamed-chunk-22-1.png │ ├── README-unnamed-chunk-22-2.png │ ├── README-unnamed-chunk-23-1.png │ ├── README-unnamed-chunk-23-2.png │ ├── README-unnamed-chunk-24-1.png │ ├── README-unnamed-chunk-25-1.png │ ├── README-unnamed-chunk-26-1.png │ ├── README-unnamed-chunk-27-1.png │ ├── README-unnamed-chunk-31-1.png │ ├── README-unnamed-chunk-9-1.png │ ├── ReporterScore.png │ └── ko00780.Z_score.png ├── gene2ko.Rd ├── genedf.Rd ├── get_all_pathway_net_index.Rd ├── get_features.Rd ├── get_reporter_score.Rd ├── hsa_kegg_pathway.Rd ├── ko.test.Rd ├── load_CARDinfo.Rd ├── load_CAZy_info.Rd ├── load_Enzyme_info.Rd ├── load_GOlist.Rd ├── load_all_pathway_NS.Rd ├── load_htable.Rd ├── load_pathway_xml_ls.Rd ├── mmu_kegg_pathway.Rd ├── modify_description.Rd ├── parse_enzyme_dat.Rd ├── pathway_net_index.Rd ├── pipe.Rd ├── plot.cm_res.Rd ├── plot_KEGG_map.Rd ├── plot_enrich_res.Rd ├── plot_features_box.Rd ├── plot_features_distribution.Rd ├── plot_features_heatmap.Rd ├── plot_features_in_pathway.Rd ├── plot_features_network.Rd ├── plot_htable.Rd ├── plot_pathway_net.Rd ├── plot_report.Rd ├── plot_report_circle_packing.Rd ├── plot_significance.Rd ├── print.reporter_score.Rd ├── print.rs_by_cm.Rd ├── pvalue2zs.Rd ├── reporter_score.Rd ├── reporter_score_res.Rd ├── up_level_KO.Rd ├── update_CARDinfo.Rd ├── update_CAZy_info.Rd ├── update_Enzyme_info.Rd ├── update_GOlist.Rd ├── update_KEGG.Rd ├── update_all_pathway_NS.Rd └── update_pathway_xml_ls.Rd ├── pkgdown └── favicon │ ├── android-chrome-192x192.png │ ├── android-chrome-512x512.png │ ├── apple-touch-icon.png │ ├── browserconfig.xml │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon.ico │ ├── mstile-150x150.png │ └── site.webmanifest └── vignettes └── ReporterScore.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/.github/workflows/R-CMD-check.yaml -------------------------------------------------------------------------------- /.github/workflows/pkgdown.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/.github/workflows/pkgdown.yaml -------------------------------------------------------------------------------- /.github/workflows/pr-commands.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/.github/workflows/pr-commands.yaml -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/ReporterScore-package.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/ReporterScore-package.R -------------------------------------------------------------------------------- /R/calculation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/calculation.R -------------------------------------------------------------------------------- /R/check_files.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/check_files.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/data.R -------------------------------------------------------------------------------- /R/enrichment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/enrichment.R -------------------------------------------------------------------------------- /R/kegg_net.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/kegg_net.R -------------------------------------------------------------------------------- /R/plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/plot.R -------------------------------------------------------------------------------- /R/print.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/print.R -------------------------------------------------------------------------------- /R/utils-pipe.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/R/utils-pipe.R -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/README.Rmd -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/README.md -------------------------------------------------------------------------------- /README_zh_CN.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/README_zh_CN.md -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/_pkgdown.yml -------------------------------------------------------------------------------- /data/CPDlist.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/CPDlist.rda -------------------------------------------------------------------------------- /data/Compound_htable.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/Compound_htable.rda -------------------------------------------------------------------------------- /data/KO_abundance_test.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/KO_abundance_test.rda -------------------------------------------------------------------------------- /data/KO_htable.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/KO_htable.rda -------------------------------------------------------------------------------- /data/KOlist.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/KOlist.rda -------------------------------------------------------------------------------- /data/Module_htable.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/Module_htable.rda -------------------------------------------------------------------------------- /data/Pathway_htable.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/Pathway_htable.rda -------------------------------------------------------------------------------- /data/genedf.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/genedf.rda -------------------------------------------------------------------------------- /data/hsa_kegg_pathway.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/hsa_kegg_pathway.rda -------------------------------------------------------------------------------- /data/mmu_kegg_pathway.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/mmu_kegg_pathway.rda -------------------------------------------------------------------------------- /data/reporter_score_res.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/data/reporter_score_res.rda -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/inst/CITATION -------------------------------------------------------------------------------- /man/CPDlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/CPDlist.Rd -------------------------------------------------------------------------------- /man/Compound_htable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/Compound_htable.Rd -------------------------------------------------------------------------------- /man/GOlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/GOlist.Rd -------------------------------------------------------------------------------- /man/KO_abundance.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_abundance.Rd -------------------------------------------------------------------------------- /man/KO_enrich.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_enrich.Rd -------------------------------------------------------------------------------- /man/KO_fisher.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_fisher.Rd -------------------------------------------------------------------------------- /man/KO_gsa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_gsa.Rd -------------------------------------------------------------------------------- /man/KO_gsea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_gsea.Rd -------------------------------------------------------------------------------- /man/KO_gsva.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_gsva.Rd -------------------------------------------------------------------------------- /man/KO_htable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_htable.Rd -------------------------------------------------------------------------------- /man/KO_padog.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_padog.Rd -------------------------------------------------------------------------------- /man/KO_safe.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_safe.Rd -------------------------------------------------------------------------------- /man/KO_sea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KO_sea.Rd -------------------------------------------------------------------------------- /man/KOlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/KOlist.Rd -------------------------------------------------------------------------------- /man/Module_htable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/Module_htable.Rd -------------------------------------------------------------------------------- /man/Pathway_htable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/Pathway_htable.Rd -------------------------------------------------------------------------------- /man/RSA_by_cm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/RSA_by_cm.Rd -------------------------------------------------------------------------------- /man/ReporterScore-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/ReporterScore-package.Rd -------------------------------------------------------------------------------- /man/c_means.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/c_means.Rd -------------------------------------------------------------------------------- /man/c_net_from_pathway_xml.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/c_net_from_pathway_xml.Rd -------------------------------------------------------------------------------- /man/calculate_NS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/calculate_NS.Rd -------------------------------------------------------------------------------- /man/calculate_ZN_score.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/calculate_ZN_score.Rd -------------------------------------------------------------------------------- /man/combine_rs_res.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/combine_rs_res.Rd -------------------------------------------------------------------------------- /man/custom_modulelist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/custom_modulelist.Rd -------------------------------------------------------------------------------- /man/custom_modulelist_from_org.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/custom_modulelist_from_org.Rd -------------------------------------------------------------------------------- /man/export_report_table.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/export_report_table.Rd -------------------------------------------------------------------------------- /man/figures/1-workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/1-workflow.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-11-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-11-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-12-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-12-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-13-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-13-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-14-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-14-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-15-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-15-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-16-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-16-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-17-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-17-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-18-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-18-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-19-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-19-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-19-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-19-2.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-20-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-20-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-20-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-20-2.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-21-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-21-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-21-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-21-2.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-22-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-22-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-22-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-22-2.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-23-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-23-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-23-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-23-2.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-24-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-24-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-25-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-25-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-26-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-26-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-27-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-27-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-31-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-31-1.png -------------------------------------------------------------------------------- /man/figures/README-unnamed-chunk-9-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/README-unnamed-chunk-9-1.png -------------------------------------------------------------------------------- /man/figures/ReporterScore.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/ReporterScore.png -------------------------------------------------------------------------------- /man/figures/ko00780.Z_score.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/figures/ko00780.Z_score.png -------------------------------------------------------------------------------- /man/gene2ko.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/gene2ko.Rd -------------------------------------------------------------------------------- /man/genedf.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/genedf.Rd -------------------------------------------------------------------------------- /man/get_all_pathway_net_index.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/get_all_pathway_net_index.Rd -------------------------------------------------------------------------------- /man/get_features.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/get_features.Rd -------------------------------------------------------------------------------- /man/get_reporter_score.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/get_reporter_score.Rd -------------------------------------------------------------------------------- /man/hsa_kegg_pathway.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/hsa_kegg_pathway.Rd -------------------------------------------------------------------------------- /man/ko.test.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/ko.test.Rd -------------------------------------------------------------------------------- /man/load_CARDinfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/load_CARDinfo.Rd -------------------------------------------------------------------------------- /man/load_CAZy_info.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/load_CAZy_info.Rd -------------------------------------------------------------------------------- /man/load_Enzyme_info.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/load_Enzyme_info.Rd -------------------------------------------------------------------------------- /man/load_GOlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/load_GOlist.Rd -------------------------------------------------------------------------------- /man/load_all_pathway_NS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/load_all_pathway_NS.Rd -------------------------------------------------------------------------------- /man/load_htable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/load_htable.Rd -------------------------------------------------------------------------------- /man/load_pathway_xml_ls.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/load_pathway_xml_ls.Rd -------------------------------------------------------------------------------- /man/mmu_kegg_pathway.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/mmu_kegg_pathway.Rd -------------------------------------------------------------------------------- /man/modify_description.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/modify_description.Rd -------------------------------------------------------------------------------- /man/parse_enzyme_dat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/parse_enzyme_dat.Rd -------------------------------------------------------------------------------- /man/pathway_net_index.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/pathway_net_index.Rd -------------------------------------------------------------------------------- /man/pipe.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/pipe.Rd -------------------------------------------------------------------------------- /man/plot.cm_res.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot.cm_res.Rd -------------------------------------------------------------------------------- /man/plot_KEGG_map.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_KEGG_map.Rd -------------------------------------------------------------------------------- /man/plot_enrich_res.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_enrich_res.Rd -------------------------------------------------------------------------------- /man/plot_features_box.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_features_box.Rd -------------------------------------------------------------------------------- /man/plot_features_distribution.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_features_distribution.Rd -------------------------------------------------------------------------------- /man/plot_features_heatmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_features_heatmap.Rd -------------------------------------------------------------------------------- /man/plot_features_in_pathway.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_features_in_pathway.Rd -------------------------------------------------------------------------------- /man/plot_features_network.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_features_network.Rd -------------------------------------------------------------------------------- /man/plot_htable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_htable.Rd -------------------------------------------------------------------------------- /man/plot_pathway_net.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_pathway_net.Rd -------------------------------------------------------------------------------- /man/plot_report.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_report.Rd -------------------------------------------------------------------------------- /man/plot_report_circle_packing.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_report_circle_packing.Rd -------------------------------------------------------------------------------- /man/plot_significance.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/plot_significance.Rd -------------------------------------------------------------------------------- /man/print.reporter_score.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/print.reporter_score.Rd -------------------------------------------------------------------------------- /man/print.rs_by_cm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/print.rs_by_cm.Rd -------------------------------------------------------------------------------- /man/pvalue2zs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/pvalue2zs.Rd -------------------------------------------------------------------------------- /man/reporter_score.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/reporter_score.Rd -------------------------------------------------------------------------------- /man/reporter_score_res.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/reporter_score_res.Rd -------------------------------------------------------------------------------- /man/up_level_KO.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/up_level_KO.Rd -------------------------------------------------------------------------------- /man/update_CARDinfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/update_CARDinfo.Rd -------------------------------------------------------------------------------- /man/update_CAZy_info.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/update_CAZy_info.Rd -------------------------------------------------------------------------------- /man/update_Enzyme_info.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/update_Enzyme_info.Rd -------------------------------------------------------------------------------- /man/update_GOlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/update_GOlist.Rd -------------------------------------------------------------------------------- /man/update_KEGG.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/update_KEGG.Rd -------------------------------------------------------------------------------- /man/update_all_pathway_NS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/update_all_pathway_NS.Rd -------------------------------------------------------------------------------- /man/update_pathway_xml_ls.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/man/update_pathway_xml_ls.Rd -------------------------------------------------------------------------------- /pkgdown/favicon/android-chrome-192x192.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/android-chrome-192x192.png -------------------------------------------------------------------------------- /pkgdown/favicon/android-chrome-512x512.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/android-chrome-512x512.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/apple-touch-icon.png -------------------------------------------------------------------------------- /pkgdown/favicon/browserconfig.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/browserconfig.xml -------------------------------------------------------------------------------- /pkgdown/favicon/favicon-16x16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/favicon-16x16.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon-32x32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/favicon-32x32.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/favicon.ico -------------------------------------------------------------------------------- /pkgdown/favicon/mstile-150x150.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/mstile-150x150.png -------------------------------------------------------------------------------- /pkgdown/favicon/site.webmanifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/pkgdown/favicon/site.webmanifest -------------------------------------------------------------------------------- /vignettes/ReporterScore.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Asa12138/ReporterScore/HEAD/vignettes/ReporterScore.Rmd --------------------------------------------------------------------------------