| signatureSearch-package | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis | 
| addGESSannot | Add Compound Annotation Info to GESS Result Table | 
| addMOA | Add MOA annotation to drug data frame | 
| add_pcid | Add PCID to drug data frame | 
| append2H5 | Append Matrix to HDF5 File | 
| build_custom_db | build_custom_db | 
| calcGseaStatBatchCpp | Calculates GSEA statistic valus for all gene sets in 'selectedStats' list. | 
| cellNtestPlot | Number of Tests in Cell Types | 
| cell_info | LINCS 2017 Cell Type Information | 
| cell_info2 | LINCS 2020 Cell Type Information | 
| chembl_moa_list | MOA to Gene Mappings | 
| clue_moa_list | MOA to Drug Name Mappings | 
| comp_fea_res | Plot for Comparing Ranking Results of FEA Methods | 
| create_empty_h5 | Create Empty HDF5 File | 
| dim | Dimensions of an Object | 
| dim-method | Dimensions of an Object | 
| drugs | Extract/Assign Drug Names for feaResult | 
| drugs-method | Extract/Assign Drug Names for feaResult | 
| drugs10 | Drug Names Used in Examples | 
| drugs<- | Extract/Assign Drug Names for feaResult | 
| drugs<--method | Extract/Assign Drug Names for feaResult | 
| drug_cell_ranks | Summary ranking statistics across cell types | 
| dsea_GSEA | FEA Methods | 
| dsea_hyperG | FEA Methods | 
| dtnetplot | Drug-Target Network Visualization | 
| enrichGO2 | GO Term Enrichment with Hypergeometric Test | 
| enrichKEGG2 | KEGG Pathway Enrichment with Hypergeometric Test | 
| enrichMOA | MOA Category Enrichment with Hypergeometric Test | 
| enrichReactome | Reactome Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched Reactome pathways with FDR control from hypergeometric test. | 
| feaResult | Constructor for 'feaResult-class' | 
| feaResult-class | feaResult object | 
| GCT object | An S4 Class to Represent a GCT Object | 
| gctx2h5 | Convert GCTX to HDF5 File | 
| gessResult | Constructor for 'gessResult-class' | 
| gessResult-class | gessResult object | 
| gess_cmap | GESS Methods | 
| gess_cor | GESS Methods | 
| gess_fisher | GESS Methods | 
| gess_gcmap | GESS Methods | 
| gess_lincs | GESS Methods | 
| gess_res_vis | GESS Result Visualization | 
| getALLEG | getALLEG | 
| getDb | getDb | 
| getDEGSig | Draw GESs from Reference Database | 
| getSig | Draw GESs from Reference Database | 
| getSPsubSig | Draw GESs from Reference Database | 
| getTreats | Get Treatment Information | 
| get_targets | Target Gene/Protein IDs for Query Drugs | 
| gmt2h5 | Convert GMT to HDF5 File | 
| gseGO2 | Modified GSEA with GO Terms | 
| gseKEGG2 | Modified GSEA with KEGG | 
| gseReactome | Modified GSEA with Reactome | 
| head | Return the First Part of an Object | 
| head-method | Return the First Part of an Object | 
| lincs_expr_inst_info | Instance Information of LINCS Expression Database | 
| lincs_pert_info | LINCS 2017 Perturbation Information | 
| lincs_pert_info2 | LINCS 2020 Perturbation Information | 
| lincs_sig_info | LINCS Signature Information | 
| list2df | Named list to data frame | 
| list_rev | Reverse list | 
| mabsGO | MeanAbs Enrichment Analysis for GO | 
| mabsKEGG | MeanAbs Enrichment Analysis for KEGG | 
| mabsReactome | MeanAbs Enrichment Analysis for Reactome | 
| matrix2h5 | Write Matrix to HDF5 file | 
| meanExpr2h5 | Calculate Mean Expression Values of LINCS Level 3 Data | 
| moa_conn | Summarize GESS Results on MOA Level | 
| parse_gctx | Parse GCTX | 
| qSig | Helper Function to Construct a 'qSig' Object | 
| qSig-class | Class "qSig" | 
| rand_query_ES | Generate WTCS Null Distribution with Random Queries | 
| read_gmt | Read in gene set information from .gmt files | 
| result | Method to Extract Result Slots | 
| result-method | Method to Extract Result Slots | 
| runWF | Run the Entire GESS/FEA Workflow | 
| set_readable | Set Readable | 
| show | show method | 
| show-method | show method | 
| signatureSearch | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis | 
| sim_score_grp | Summary Scores by Groups of Cell Types | 
| tail | Return the Last Part of an Object | 
| tail-method | Return the Last Part of an Object | 
| targetList | Target Sample Data Set | 
| tarReduce | Show Reduced Targets | 
| tsea_dup_hyperG | FEA Methods | 
| tsea_mabs | FEA Methods | 
| tsea_mGSEA | FEA Methods | 
| vec_char_redu | Reduce Number of Character |