GCT object              An S4 Class to Represent a GCT Object
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
drug_cell_ranks         Summary ranking statistics across cell types
drugs                   Extract/Assign Drug Names for feaResult
drugs10                 Drug Names Used in Examples
dsea_GSEA               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
gctx2h5                 Convert GCTX to HDF5 File
gessResult              Constructor for 'gessResult-class'
gessResult-class        gessResult object
gess_cmap               GESS Methods
gess_res_vis            GESS Result Visualization
getALLEG                getALLEG
getDb                   getDb
getSig                  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
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
runWF                   Run the Entire GESS/FEA Workflow
set_readable            Set Readable
show                    show method
signatureSearch-package
                        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
tarReduce               Show Reduced Targets
targetList              Target Sample Data Set
vec_char_redu           Reduce Number of Character
