Files in jokergoo/simplifyGO
Simplify Functional Enrichment Results

.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/00_S4_generic_methods.R
R/binary_cut.R R/cluster.R R/compare_methods.R R/dend_utils.R R/foo.R R/gene_desc.R R/global.R R/ht_clusters.R R/keywords.R R/node_partition.R R/shiny.R R/similarity_DO.R R/similarity_GO.R R/similarity_by_overlap.R R/similarity_pathway.R R/simple_plot.R R/simplify.R R/stats.R R/utils.R R/word_cloud.R R/z.register_methods.R R/zzz.R README.md
_pkgdown.yml
build_pkg_site.R
docs/404.html
docs/LICENSE-text.html
docs/articles/EBI_Expression_Atlas_boxplot.svg
docs/articles/EBI_Expression_Atlas_similarity.svg
docs/articles/GO_heatmap_random_BP.jpg
docs/articles/GO_heatmap_random_BP_1.jpg
docs/articles/index.html
docs/articles/interactive.html
docs/articles/interactive_files/header-attrs-2.7/header-attrs.js
docs/articles/interactive_files/header-attrs-2.9/header-attrs.js
docs/articles/main.css
docs/articles/random_BP_boxplot.svg
docs/articles/random_BP_similarity.svg
docs/articles/simplifyEnrichment.html
docs/articles/simplifyEnrichment_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/simplifyEnrichment_files/anchor-sections-1.0/anchor-sections.css
docs/articles/simplifyEnrichment_files/anchor-sections-1.0/anchor-sections.js
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docs/articles/simplifyEnrichment_files/header-attrs-2.5/header-attrs.js
docs/articles/simplifyEnrichment_files/header-attrs-2.7/header-attrs.js
docs/articles/simplifyEnrichment_files/header-attrs-2.9/header-attrs.js
docs/articles/simplifyGO.html
docs/articles/simplifyGO_files/figure-html/unnamed-chunk-16-1.png
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docs/articles/simplifyGO_files/figure-html/unnamed-chunk-7-1.png
docs/articles/simplifyGO_files/header-attrs-2.1/header-attrs.js
docs/articles/word_cloud_anno.html
docs/articles/word_cloud_anno_files/accessible-code-block-0.0.1/empty-anchor.js
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docs/articles/word_cloud_anno_files/anchor-sections-1.0/anchor-sections.js
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docs/articles/word_cloud_anno_files/header-attrs-2.5/header-attrs.js
docs/articles/word_cloud_anno_files/header-attrs-2.7/header-attrs.js
docs/articles/word_cloud_anno_files/header-attrs-2.9/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/DO_similarity.html
docs/reference/GO_similarity.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/all_clustering_methods.html
docs/reference/anno_word_cloud-1.png
docs/reference/anno_word_cloud.html
docs/reference/anno_word_cloud_from_GO.html
docs/reference/area_above_ecdf.html
docs/reference/binary_cut.html
docs/reference/cluster_GO.html
docs/reference/cluster_by_MCL.html
docs/reference/cluster_by_apcluster.html
docs/reference/cluster_by_dynamicTreeCut.html
docs/reference/cluster_by_hdbscan.html
docs/reference/cluster_by_igraph.html
docs/reference/cluster_by_kmeans.html
docs/reference/cluster_by_mclust.html
docs/reference/cluster_by_pam.html
docs/reference/cluster_terms.html
docs/reference/cmp_make_clusters.html
docs/reference/cmp_make_plot-1.png
docs/reference/cmp_make_plot-2.png
docs/reference/cmp_make_plot.html
docs/reference/compare_clustering_methods-1.png
docs/reference/compare_clustering_methods-2.png
docs/reference/compare_clustering_methods.html
docs/reference/compare_methods-1.png
docs/reference/compare_methods-2.png
docs/reference/compare_methods.html
docs/reference/compare_methods_make_clusters.html
docs/reference/compare_methods_make_plot.html
docs/reference/count_word.html
docs/reference/count_word_from_GO.html
docs/reference/count_words.html
docs/reference/dend_node_apply.html
docs/reference/difference_score.html
docs/reference/edit_node.html
docs/reference/export_to_shiny_app.html
docs/reference/guess_ont.html
docs/reference/heightDetails.word_cloud.html
docs/reference/ht_GO_clusters-1.png
docs/reference/ht_GO_clusters.html
docs/reference/ht_clusters-1.png
docs/reference/ht_clusters-2.png
docs/reference/ht_clusters.html
docs/reference/index.html
docs/reference/keyword_enrichment_from_GO.html
docs/reference/partition_by_hclust.html
docs/reference/partition_by_kmeans.html
docs/reference/partition_by_kmeanspp.html
docs/reference/partition_by_pam.html
docs/reference/plot_binary_cut-1.png
docs/reference/plot_binary_cut-2.png
docs/reference/plot_binary_cut-3.png
docs/reference/plot_binary_cut.html
docs/reference/random_DO.html
docs/reference/random_GO.html
docs/reference/register_clustering_methods.html
docs/reference/remove_clustering_methods.html
docs/reference/reset_clustering_methods.html
docs/reference/scale_fontsize.html
docs/reference/se_opt.html
docs/reference/select_cutoff-1.png
docs/reference/select_cutoff.html
docs/reference/simplifyEnrichment.html
docs/reference/simplifyGO-1.png
docs/reference/simplifyGO.html
docs/reference/simplifyGOFromMultipleLists-1.png
docs/reference/simplifyGOFromMultipleLists-2.png
docs/reference/simplifyGOFromMultipleLists-3.png
docs/reference/simplifyGOFromMultipleLists.html
docs/reference/subset_enrichResult.html
docs/reference/term_similarity.html
docs/reference/term_similarity_from_KEGG.html
docs/reference/term_similarity_from_MSigDB.html
docs/reference/term_similarity_from_Reactome.html
docs/reference/term_similarity_from_enrichResult.html
docs/reference/term_similarity_from_gmt.html
docs/reference/widthDetails.word_cloud.html
docs/reference/word_cloud_grob-1.png
docs/reference/word_cloud_grob-2.png
docs/reference/word_cloud_grob-3.png
docs/reference/word_cloud_grob-4.png
docs/reference/word_cloud_grob.html
docs/sitemap.xml
inst/CITATION
inst/extdata/E-GEOD-101794_g2_g1_diff_gene_list.txt
inst/extdata/GO_global_word_freq.rds
inst/extdata/gene_desc_black_list.txt
inst/extdata/golub_sig_go.RData
inst/extdata/pathway_network_kegg.rds
inst/extdata/pathway_network_panther.rds
inst/extdata/pathway_network_pathbank.rds
inst/extdata/pathway_network_reactome.rds
inst/extdata/random_GO_BP_sim_mat.rds
inst/extdata/random_GO_BP_sim_mat_clt.rds
inst/extdata/refseq_gene_desc_human.rds
inst/extdata/tdm_GO.rds
man/DO_similarity.Rd man/GO_similarity.Rd man/all_clustering_methods.Rd man/anno_word_cloud.Rd man/anno_word_cloud_from_GO.Rd man/area_above_ecdf.Rd man/binary_cut.Rd man/cluster_by_MCL.Rd man/cluster_by_apcluster.Rd man/cluster_by_dynamicTreeCut.Rd man/cluster_by_hdbscan.Rd man/cluster_by_igraph.Rd man/cluster_by_kmeans.Rd man/cluster_by_mclust.Rd man/cluster_by_pam.Rd man/cluster_terms.Rd man/cmp_make_clusters.Rd man/cmp_make_plot.Rd man/compare_clustering_methods.Rd man/count_words.Rd man/dend_node_apply.Rd man/difference_score.Rd man/edit_node.Rd man/export_to_shiny_app.Rd man/guess_ont.Rd man/heightDetails.word_cloud.Rd man/ht_clusters.Rd man/keyword_enrichment_from_GO.Rd man/partition_by_hclust.Rd man/partition_by_kmeans.Rd man/partition_by_kmeanspp.Rd man/partition_by_pam.Rd man/plot_binary_cut.Rd man/random_DO.Rd man/random_GO.Rd man/register_clustering_methods.Rd man/remove_clustering_methods.Rd man/reset_clustering_methods.Rd man/scale_fontsize.Rd man/se_opt.Rd man/select_cutoff.Rd man/simplifyEnrichment.Rd man/simplifyGO.Rd man/simplifyGOFromMultipleLists.Rd man/subset_enrichResult.Rd man/summarizeGO.Rd man/term_similarity.Rd man/term_similarity_from_KEGG.Rd man/term_similarity_from_MSigDB.Rd man/term_similarity_from_Reactome.Rd man/term_similarity_from_enrichResult.Rd man/term_similarity_from_gmt.Rd man/widthDetails.word_cloud.Rd man/word_cloud_grob.Rd tests/test-all.R tests/testthat/test_GO_similarity.R tests/testthat/test_cluster_mat.R tests/testthat/test_dend_utils.R tests/testthat/test_register.R tests/testthat/test_sim.R tests_not_run/test.R tests_not_run/test2.R vignettes/interactive.Rmd
vignettes/main.css
vignettes/simplifyEnrichment.Rmd vignettes/word_cloud_anno.Rmd
jokergoo/simplifyGO documentation built on Oct. 25, 2023, 9:02 p.m.