Man pages for ReporterScore
Generalized Reporter Score-Based Enrichment Analysis for Omics Data
| c_means | 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 |
| gene2ko | Transfer gene symbol table to KO table |
| genedf | human gene table |
| get_features | get features in a modulelist |
| get_reporter_score | Calculate reporter score |
| GOlist | The GOlist used for enrichment. |
| hsa_kegg_pathway | pathway information for "hsa" |
| 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' |
| KOlist | The KOlist used for enrichment. |
| KO_padog | Perform Pathway Analysis with Down-weighting of Overlapping... |
| KO_safe | Perform Significance Analysis of Function and Expression |
| KO_sea | Perform Simultaneous Enrichment Analysis |
| ko.test | Differential analysis or Correlation analysis for... |
| load_CARDinfo | Load the CARDinfo (from CARD database) |
| load_GOlist | Load the GOlist (from 'GO' database) |
| load_htable | Load the specific table (from 'KEGG') |
| 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' |
| pipe | Pipe operator |
| plot.cm_res | Plot c_means result |
| 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_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... |
| ReporterScore-package | ReporterScore: Generalized Reporter Score-Based Enrichment... |
| reporter_score_res | 'reporter_score()' result from KO_abundance_test |
| RSA_by_cm | Reporter score analysis after C-means clustering |
| update_CARDinfo | update CARDinfo from (from 'CARD' database) |
| update_GOlist | Update the GO2gene files (from 'GO' database) |
| update_KEGG | Update files from 'KEGG' |
| up_level_KO | Upgrade the KO level |
