Man pages for CityUHK-CompBio/HTSanalyzeR2
HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data
| analyze | Gene Set Collection Analysis or NetWork Analysis |
| analyzeGscaTS | Gene Set Collection Analysis for Time-series data. |
| analyzeNwaTS | Subnetwork analysis for Time-series data |
| annotationConvertor | Convert between different types of gene identifiers |
| appendGSTerms | Append gene set terms to GSCA results and gene names... |
| appendGSTermsTS | Append gene set terms to GSCA results for each GSCA object of... |
| Biogrid_HS_Interactome | An object of class 'igraph' |
| Biogrid_HS_Mat | An interactome matrix for _Homo Sapiens_ |
| cellHTS2OutputStatTests | Perform statistical tests on a cellHTS object |
| d7 | CRISPR data set |
| d7_gsca | An object of class 'GSCA' |
| d7_nwa | An object of class 'NWA' |
| duplicateRemover | Remove duplicates in a named vector of phenotypes. |
| extractEnrichMap-GSCA-method | Extract the enrichment map as an igraph object |
| extractSubNet-NWA-method | Extract the subnetwork as an igraph object |
| forceGraph | Create a force-directed graph widget |
| getInteractome | Accessors for the 'interactome' slot of a 'NWA' object. |
| getPara | Accessors for the 'para' slot of a 'GSCA' or 'fdr' slot of a... |
| getResult | Accessors for the 'result' slot of a 'GSCA' or 'NWA' object. |
| getSummary | Accessors for the 'summary' slot of a 'GSCA' or 'NWA' object. |
| getTopGeneSets | Select top significant gene sets from results of GSCA object |
| GOGeneSets | Create a list of gene sets based on Gene Ontology terms |
| GSCA | An S4 class for Gene Set Collection Analyses on... |
| GSCABatch | An S4 class for Time series data packaging in Gene Set... |
| gscaTS | A list of 'GSCA' object |
| GSE33113_exp | Expression of a demo data: GSE33113 |
| GSE33113_label | Concensus molecular subtype label of GSE33113 |
| GSE33113_limma | limma result of a gene expression data |
| HTSanalyzeR2 | HTSanalyzeR2 Package Overview |
| HTSanalyzeR2Pipe | An analysis pipeline for common phenotype data |
| HTSanalyzeR4MAGeCK | An analysis pipeline for CRISPR data preprocessed by MAGeCK |
| interactome | Create an interactome from BioGRID database or input custom... |
| interactomeNwaTS | Create an interactome from BioGRID database or input custom... |
| KeggGeneSets | Create a list of KEGG gene sets |
| MSigDBGeneSets | Create a list of gene sets for specific species from MSigDB... |
| NWA | An S4 class for NetWork Analysis on high-throughput data |
| NWABatch | An S4 class for Time series data package in NetWork Analysis... |
| nwaTS | A list of 'NWA' object |
| plotGSEA | Plot and save figures of GSEA results for top significant... |
| preprocess | A preprocessing method for objects of class GSCA or NWA |
| preprocessGscaTS | A preprocessing method for a GSCABatch object of Time-series... |
| preprocessNwaTS | A preprocessing method for a GSCABatch object of Time-series... |
| report | Write HTML reports for enrichment or network analyses |
| reportAll | Write HTML reports for both enrichment and network analyses |
| summarize | Print summary information for an object of class GSCA or NWA |
| viewEnrichMap-GSCA-method | Plot the enrichment map for GSEA or GSOA result |
| viewGSEA | Plot a figure of GSEA results for one gene set |
| viewSubNet-NWA-method | Plot the identified subnetwork of an NWA object |
| xn | An object of class 'cellHTS2' |
