signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis9 months ago
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