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Package index

All functions

getDEAInfo(<DeeDeeExperiment>) `getDEAInfo<-`(<DeeDeeExperiment>) getDEANames(<DeeDeeExperiment>) renameDEA(<DeeDeeExperiment>) addDEA(<DeeDeeExperiment>) removeDEA(<DeeDeeExperiment>) getDEA(<DeeDeeExperiment>) getDEAList(<DeeDeeExperiment>) addScenarioInfo(<DeeDeeExperiment>) getFEAInfo(<DeeDeeExperiment>) `getFEAInfo<-`(<DeeDeeExperiment>) getFEANames(<DeeDeeExperiment>) renameFEA(<DeeDeeExperiment>) addFEA(<DeeDeeExperiment>) removeFEA(<DeeDeeExperiment>) getFEA(<DeeDeeExperiment>) getFEAList(<DeeDeeExperiment>) linkDEAandFEA(<DeeDeeExperiment>)
Methods for DeeDeeExperiment objects
show(<DeeDeeExperiment>) summary(<DeeDeeExperiment>)
Miscellaneous DeeDeeExperiment methods
DeeDeeExperiment-package DeeDeeExperiment-pkg
DeeDeeExperiment
DeeDeeExperiment()
The DeeDeeExperiment class
IFNg_both
A sample DESeqResults object
IFNg_naive
A sample DESeqResults object
Salm_both
A sample DESeqResults object
Salm_naive
A sample DESeqResults object
clusterPro_res
clusterPro_res
dd_list_original
dd_list_original
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
export_result_for_dde()
Export DEA/FEA/ASSAY results from a DeeDeeExperiment to excel files
fgseaRes
fgseaRes
gost_res
gost_res
gsea_res
gsea_res
limma_list_for_dde()
Convert a MArrayLM object with multiple contrasts into a list of DE results tables compatible with DeeDeeExperiment
muscat_list_for_dde()
Convert muscat::pbDS() results into a flat list of data frames compatible with DeeDeeExperiment
muscat_res
muscat_res
supported_fea_formats()
Display available FEA formats
topGO_results_list
topGO_results_list