CPDlist                 The CPDlist used for enrichment.
Compound_htable         Compound htable from 'KEGG'
GOlist                  The GOlist used for enrichment.
KO_abundance            The KOs abundance table and group table.
KO_enrich               Perform enrichment analysis
KO_fisher               Perform fisher's exact enrichment analysis
KO_gsa                  Perform gene set analysis
KO_gsea                 Perform gene set enrichment analysis
KO_gsva                 Perform Gene Set Variation Analysis
KO_htable               KO htable from 'KEGG'
KO_padog                Perform Pathway Analysis with Down-weighting of
                        Overlapping Genes (PADOG)
KO_safe                 Perform Significance Analysis of Function and
                        Expression
KO_sea                  Perform Simultaneous Enrichment Analysis
KOlist                  The KOlist used for enrichment.
Module_htable           Module htable from 'KEGG'
Pathway_htable          Pathway htable from 'KEGG'
RSA_by_cm               Reporter score analysis after C-means
                        clustering
c_net_from_pathway_xml
                        Create a network from KEGG pathway XML files
cm_test_k               Test the proper clusters k for c_means
combine_rs_res          Combine the results of 'step by step GRSA'
custom_modulelist       Build a custom modulelist
custom_modulelist_from_org
                        Custom modulelist from a specific organism
export_report_table     Export report score result tables
gene2ko                 Transfer gene symbol table to KO table
genedf                  human gene table
get_all_pathway_net_index
                        Create an index for all KEGG pathway networks
get_features            get features in a modulelist
get_reporter_score      Calculate reporter score
hsa_kegg_pathway        pathway information for "hsa"
ko.test                 Differential analysis or Correlation analysis
                        for KO-abundance table
load_CARDinfo           Load the CARDinfo (from CARD database)
load_CAZy_info          Load the CAZy_info (from CAZy database)
load_Enzyme_info        Load the Enzyme_info (from ExPASy Enzyme
                        database)
load_GOlist             Load the GOlist (from 'GO' database)
load_htable             Load the specific table (from 'KEGG')
load_pathway_xml_ls     Load KEGG pathway XML file list
mmu_kegg_pathway        pathway information for "mmu"
modify_description      Modify the pathway description before plotting
parse_enzyme_dat        Parse enzyme.dat file into a structured data
                        frame
pathway_net_index       Create a pathway network index data.frame
plot.cm_res             Plot c_means result
plot_KEGG_map           plot_KEGG_map
plot_enrich_res         Plot enrich_res
plot_features_box       Plot features boxplot
plot_features_distribution
                        plot the Z-score of features distribution
plot_features_heatmap   Plot features heatmap
plot_features_in_pathway
                        Plot features trend in one pathway or module
plot_features_network   Plot features network
plot_htable             Plot htable levels
plot_pathway_net        Plot a KEGG pathway network
plot_report             Plot the reporter_res
plot_report_circle_packing
                        Plot the reporter_res as circle_packing
plot_significance       Plot the significance of pathway
print.reporter_score    Print reporter_score
print.rs_by_cm          Print rs_by_cm
pvalue2zs               Transfer p-value of KOs to Z-score
reporter_score          One step to get the reporter score of your KO
                        abundance table.
reporter_score_res      'reporter_score()' result from
                        KO_abundance_test
up_level_KO             Upgrade the KO level
update_CARDinfo         update CARDinfo from (from 'CARD' database)
update_CAZy_info        Update CAZy_info from CAZy database
update_Enzyme_info      Update Enzyme_info from ExPASy Enzyme database
update_GOlist           Update the GO2gene files (from 'GO' database)
update_KEGG             Update files from 'KEGG'
update_pathway_xml_ls   Download KEGG pathway XML files and create
                        networks
