Man pages for HTSanalyzeR
Gene set over-representation, enrichment and network analyses for high-throughput screens
| aggregatePvals | Aggregate p-values from gene set over-representation tests. |
| analyze | Gene Set Collection Analysis or NetWork Analysis |
| analyzeGeneSetCollections | Hypergeometric tests and Gene Set Enrichment Analyses over a... |
| annotationConvertor | Convert between different types of gene identifiers |
| appendGSTerms | Append gene set terms to GSCA results |
| biogridDataDownload | Download and extract a network interaction matrix from a... |
| celAnnotationConvertor | Convert between different types of gene identifiers for... |
| cellHTS2OutputStatTests | Perform statistical tests on a cellHTS object |
| changes | View new changes made in the latest version |
| collectionGsea | Compute observed and permutation-based enrichment scores for... |
| data-KcViab | A Sample data set of the package HTSanalyzeR |
| drosoAnnotationConvertor | Convert between different types of gene identifiers for... |
| duplicateRemover | Remove duplicates in a named vector of phenotypes |
| FDRcollectionGsea | Compute the GSEA false discovery rates for a collection... |
| GenHTSAHtmlRowUnit | Generate html codes for one unit of a row of a table |
| getTopGeneSets | Select top significant gene sets from GSEA results |
| GOGeneSets | Create a list of gene sets based on GO terms |
| GSCA-class | An S4 class for Gene Set Collection Analyses on... |
| gseaPlots | Plot GSEA results for one gene set |
| gseaScores | Compute enrichment scores for GSEA (Gene Set Enrichment... |
| htmlAttrVectorPaste | Collapse an attribute vector for a table unit |
| HTSanalyzeR | HTSanalyzeR Package Overview |
| HTSanalyzeR4cellHTS2 | An analysis pipeline for cellHTS2 objects |
| hyperGeoTest | Performs hypergeometric tests for over-representation... |
| interactome | Create an interactome from BioGRID data sets |
| KeggGeneSets | Create a list of gene sets based on KEGG pathways terms |
| makeGSEAplots | Produce GSEA plots |
| makeOverlapTable | Find and save the overlapped genes between a gene set and a... |
| mammalAnnotationConvertor | Convert between different types of identifiers for mammalian... |
| multiHyperGeoTest | Hypergeometric tests on a list of gene sets |
| networkAnalysis | Identify enriched subnetworks |
| networkPlot | Plot the enriched subnetwork |
| NWA-class | An S4 class for NetWork Analysis on high-throughput screens |
| pairwiseGsea | GSEA on a pair of phenotypes |
| pairwiseGseaPlot | Produce a plot for pairwise GSEA result on one gene set |
| pairwisePhenoMannWhit | Mann-Whitney U test for shift in location of genes from gene... |
| paraCheck | Check parameters |
| permutationPvalueCollectionGsea | Compute the GSEA p-values for a list of gene sets |
| plotEnrichMap | Plot and save an enrichment map for results of GSEA or... |
| plotGSEA | Plot and save figures of GSEA results for top significant... |
| plotSubNet | Plot and save a figure of the enriched subnetwork |
| preprocess | A preprocessing method for objects of class GSCA or NWA |
| report | Write HTML reports for enrichment or network analyses |
| reportAll | Write HTML reports for both the enrichment and network... |
| summarize | Print summary information for an object of class GSCA or NWA |
| viewEnrichMap | Plot a figure of the enrichment map for GSEA or... |
| viewGSEA | Plot a figure of GSEA results for one gene set |
| viewSubNet | Plot a figure of the enriched subnetwork |
| writeHTSAHtmlHead | Write the head part of report htmls |
| writeHTSAHtmlSummary | Write the summary part of report htmls |
| writeHTSAHtmlTab | Write tabs to report htmls |
| writeHTSAHtmlTable | Write a table to report htmls |
| writeHTSAHtmlTail | Write the tail part of report htmls |
| writeReportHTSA | Write HTML reports for enrichment and/or network analyses |
