Man pages for yduan004/signatureSearch
Environment for Gene Expression 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... |
| cell_info | LINCS 2017 Cell Type Information |
| cell_info2 | LINCS 2020 Cell Type Information |
| cellNtestPlot | Number of Tests in Cell Types |
| 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-methods | Dimensions of an Object |
| drug_cell_ranks | Summary ranking statistics across cell types |
| drugs10 | Drug Names Used in Examples |
| drugs-methods | Extract/Assign Drug Names for feaResult |
| 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... |
| fea | FEA Methods |
| 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 |
| gess | GESS Methods |
| gessResult | Constructor for 'gessResult-class' |
| gessResult-class | gessResult object |
| gess_res_vis | GESS Result Visualization |
| getALLEG | getALLEG |
| getDb | getDb |
| getSig | Draw GESs from Reference Database |
| get_targets | Target Gene/Protein IDs for Query Drugs |
| getTreats | Get Treatment Information |
| gmt2h5 | Convert GMT to HDF5 File |
| gseGO2 | Modified GSEA with GO Terms |
| gseKEGG2 | Modified GSEA with KEGG |
| gseReactome | Modified GSEA with Reactome |
| head-methods | 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-methods | Method to Extract Result Slots |
| runWF | Run the Entire GESS/FEA Workflow |
| set_readable | Set Readable |
| show-methods | show method |
| signatureSearch-package | Environment for Gene Expression Signature Searching Combined... |
| sim_score_grp | Summary Scores by Groups of Cell Types |
| tail-methods | Return the Last Part of an Object |
| targetList | Target Sample Data Set |
| tarReduce | Show Reduced Targets |
| vec_char_redu | Reduce Number of Character |
