as.enrich_res |
Perform enrichment analysis |
cm_test_k |
Test the proper clusters k for c_means |
combine_rs_res |
Combine the results of 'step by step GRSA' |
Compound_htable |
Compound htable from 'KEGG' |
CPDlist |
The CPDlist used for enrichment. |
custom_modulelist |
Build a custom modulelist |
custom_modulelist_from_org |
Custom modulelist from a specific organism |
c_means |
Test the proper clusters k for c_means |
download_org_pathway |
Update files from 'KEGG' |
extract_cluster |
Reporter score analysis after C-means clustering |
gene2ko |
Transfer gene symbol table to KO table |
genedf |
human gene table |
get_features |
get features in a modulelist |
get_KOs |
get features in a modulelist |
get_org_pathway |
Update files from 'KEGG' |
get_reporter_score |
Calculate reporter score |
GOlist |
The GOlist used for enrichment. |
GRSA |
One step to get the reporter score of your KO abundance table. |
GRSA_by_cm |
Reporter score analysis after C-means clustering |
hsa_kegg_pathway |
pathway information for "hsa" |
ko.test |
Differential analysis or Correlation analysis for KO-abundance table |
KOlist |
The KOlist 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 |
load_CARDinfo |
Load the CARDinfo (from CARD database) |
load_Compound_htable |
Load the specific table (from 'KEGG') |
load_CPDlist |
Load the specific table (from 'KEGG') |
load_GOinfo |
Load the GOlist (from 'GO' database) |
load_GOlist |
Load the GOlist (from 'GO' database) |
load_htable |
Load the specific table (from 'KEGG') |
load_KOlist |
Load the specific table (from 'KEGG') |
load_KO_desc |
Load the specific table (from 'KEGG') |
load_KO_htable |
Load the specific table (from 'KEGG') |
load_Module_htable |
Load the specific table (from 'KEGG') |
load_org_pathway |
Load the specific table (from 'KEGG') |
load_Pathway_htable |
Load the specific table (from 'KEGG') |
metadata |
The KOs abundance table and group table. |
mmu_kegg_pathway |
pathway information for "mmu" |
modify_description |
Modify the pathway description before plotting |
Module_htable |
Module htable from 'KEGG' |
Pathway_htable |
Pathway htable from 'KEGG' |
plot.cm_res |
Plot c_means result |
plot.enrich_res |
Plot enrich_res |
plot_c_means |
Reporter score analysis after C-means clustering |
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_KEGG_map |
plot_KEGG_map |
plot_KOs_box |
Plot features boxplot |
plot_KOs_distribution |
plot the Z-score of features distribution |
plot_KOs_heatmap |
Plot features heatmap |
plot_KOs_in_pathway |
Plot features trend in one pathway or module |
plot_KOs_network |
Plot features network |
plot_report |
Plot the reporter_res |
plot_report_bar |
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 |
reporter_score_res2 |
'reporter_score()' result from KO_abundance_test |
RSA |
One step to get the reporter score of your KO abundance table. |
RSA_by_cm |
Reporter score analysis after C-means clustering |
transform_modulelist |
Build a custom modulelist |
update_CARDinfo |
update CARDinfo from (from 'CARD' database) |
update_GOinfo |
Update the GO2gene files (from 'GO' database) |
update_GOlist |
Update the GO2gene files (from 'GO' database) |
update_htable |
Update files from 'KEGG' |
update_KEGG |
Update files from 'KEGG' |
update_KO_file |
Update files from 'KEGG' |
update_org_pathway |
Update files from 'KEGG' |
up_level_KO |
Upgrade the KO level |