DeeDeeExperiment: An S4 Class for managing and exploring omics
analysis results
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Documentation for package ‘DeeDeeExperiment’ version 0.99.5
Help Pages
| DeeDeeExperiment-package | DeeDeeExperiment |
| .DeeDeeExperiment | The DeeDeeExperiment class |
| addDEA | Methods for DeeDeeExperiment objects |
| addDEA-method | Methods for DeeDeeExperiment objects |
| addFEA | Methods for DeeDeeExperiment objects |
| addFEA-method | Methods for DeeDeeExperiment objects |
| addScenarioInfo | Methods for DeeDeeExperiment objects |
| addScenarioInfo-method | Methods for DeeDeeExperiment objects |
| clusterPro_res | 'clusterPro_res' |
| dd_list_original | dd_list_original |
| DeeDeeExperiment | The DeeDeeExperiment class |
| DeeDeeExperiment-class | The DeeDeeExperiment class |
| DeeDeeExperiment-methods | Methods for DeeDeeExperiment objects |
| DeeDeeExperiment-misc | Miscellaneous DeeDeeExperiment methods |
| DeeDeeExperiment-pkg | DeeDeeExperiment |
| de_limma | A sample 'MArrayLM' object |
| de_named_list | de_named_list |
| dge_exact_IFNg_both | A sample 'DGEExact' object |
| dge_exact_IFNg_naive | A sample 'DGEExact' object |
| dge_exact_Salm_both | A sample 'DGEExact' object |
| dge_exact_Salm_naive | A sample 'DGEExact' object |
| dge_lrt_IFNg_both | A sample 'DGELRT' object |
| dge_lrt_IFNg_naive | A sample 'DGELRT' object |
| dge_lrt_Salm_both | A sample 'DGELRT' object |
| dge_lrt_Salm_naive | A sample 'DGELRT' object |
| enrichr_res | 'enrichr_res' |
| fgseaRes | 'fgseaRes' |
| getDEA | Methods for DeeDeeExperiment objects |
| getDEA-method | Methods for DeeDeeExperiment objects |
| getDEAInfo | Methods for DeeDeeExperiment objects |
| getDEAInfo-method | Methods for DeeDeeExperiment objects |
| getDEAInfo<- | Methods for DeeDeeExperiment objects |
| getDEAInfo<--method | Methods for DeeDeeExperiment objects |
| getDEAList | Methods for DeeDeeExperiment objects |
| getDEAList-method | Methods for DeeDeeExperiment objects |
| getDEANames | Methods for DeeDeeExperiment objects |
| getDEANames-method | Methods for DeeDeeExperiment objects |
| getFEA | Methods for DeeDeeExperiment objects |
| getFEA-method | Methods for DeeDeeExperiment objects |
| getFEAInfo | Methods for DeeDeeExperiment objects |
| getFEAInfo-method | Methods for DeeDeeExperiment objects |
| getFEAInfo<- | Methods for DeeDeeExperiment objects |
| getFEAInfo<--method | Methods for DeeDeeExperiment objects |
| getFEAList | Methods for DeeDeeExperiment objects |
| getFEAList-method | Methods for DeeDeeExperiment objects |
| getFEANames | Methods for DeeDeeExperiment objects |
| getFEANames-method | Methods for DeeDeeExperiment objects |
| gost_res | 'gost_res' |
| gsea_res | 'gsea_res' |
| IFNg_both | A sample 'DESeqResults' object |
| IFNg_naive | A sample 'DESeqResults' object |
| linkDEAandFEA | Methods for DeeDeeExperiment objects |
| linkDEAandFEA-method | Methods for DeeDeeExperiment objects |
| removeDEA | Methods for DeeDeeExperiment objects |
| removeDEA-method | Methods for DeeDeeExperiment objects |
| removeFEA | Methods for DeeDeeExperiment objects |
| removeFEA-method | Methods for DeeDeeExperiment objects |
| renameDEA | Methods for DeeDeeExperiment objects |
| renameDEA-method | Methods for DeeDeeExperiment objects |
| renameFEA | Methods for DeeDeeExperiment objects |
| renameFEA-method | Methods for DeeDeeExperiment objects |
| Salm_both | A sample 'DESeqResults' object |
| Salm_naive | A sample 'DESeqResults' object |
| show-method | Miscellaneous DeeDeeExperiment methods |
| summary-method | Miscellaneous DeeDeeExperiment methods |
| supported_fea_formats | Display available FEA formats |
| topGO_results_list | 'topGO_results_list' |