.Rbuildignore
          
        
          
            
            .github/.gitignore
          
        
          
            
            .github/workflows/R-CMD-check.yaml
          
        
          
            
            .gitignore
          
        
          
            
            DESCRIPTION
          
        
          
            
            LICENSE
          
        
          
            
            NAMESPACE
          
        
          
            
            NEWS
          
        
          
            
            R/binary_cut.R
          
        
          
            
            R/cluster.R
          
        
          
            
            R/compare_methods.R
          
        
          
            
            R/dend_utils.R
          
        
          
            
            R/global.R
          
        
          
            
            R/ht_clusters.R
          
        
          
            
            R/keywords.R
          
        
          
            
            R/node_partition.R
          
        
          
            
            R/shiny.R
          
        
          
            
            R/similarity_GO.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
          
        
          
            
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            docs/reference/DO_similarity.html
          
        
          
            
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            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
          
        
          
            
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            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
          
        
          
            
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            tests/testthat/test_dend_utils.R
          
        
          
            
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            vignettes/word_cloud_anno.Rmd