Introduction | Background | Motivation and Design | History of GES Databases | Terminology | Getting Started | Package Install | Reference Databases | Signature Searches (GESS) | Test Query and Database | CMAP Search Method | LINCS Search Method | gCMAP Search Method | Fisher Search Method | Correlation-based Search Method | CORall | CORsub | Summary of Search Results | GESS Result Visualization | Batch Processing of GESSs | Sequential Processing | Parallelization with Multiple CPU Cores | Parallelization with Multiple Computer Systems | Functional Enrichment (FEA) | TSEA | Hypergeometric Test | With GO | With Reactome | mGSEA Method | MeanAbs Method | DSEA | GSEA Method | Comparing FEA Results | Summary of FEA Results | Drug-Target Network Visualization | Run Workflow | Additional Databases | Gene Set Databases | Overview | Gene Sets as Queries | Gene Sets as Database | MSigDB | GSKB | Supplemental Material | Construction of Toy Database | Session Info | Funding | References

Introduction | Install and Load Package | Explore Data Sets | LINCS Signature Database | Z-scores from ExperimentHub | Z-scores from GEO | Download Level 5 Data | Filter Signatures | Z-score Data in HDF5 | DEG and Cutoff Definitions | Intensities from ExperimentHub | Intensities from GEO | Download Level 3 Data | Mean Intensities in HDF5 | LINCS2 Signature Database | Z-scores from CLUE | CMap2 Signature Database | Rank Matrix from ExperimentHub | Rank Matrix from Sources | Download Rank Data | Filter instances | Annotated Gene Level Data | Annotation Information | Gene Level Data | Store Rank Matrix in HDF5 file | Intensities from Sources | Custom Signature Databases | Additional Datasets | Supplemental Material | CMap2 Intensities from Sources | Directory Structure | Download of CEL Files | Determine Chip Type | Normalization of CEL Files | Average Intensities Across Replicates | CMap2 LFC database | Load from ExperimentHub | Generate from Sources | Generate list of CEL files defining treatment vs. control comparisons | DEG analysis with limma | Save the LFC and FDR matrix to an HDF5 file | Session Info | Funding | References