HTSanalyzeR-package | HTSanalyzeR Package Overview |
aggregatePvals | Aggregate p-values from gene set over-representation tests. |
analyze | Gene Set Collection Analysis or NetWork Analysis |
analyze-method | Gene Set Collection Analysis or NetWork Analysis |
analyzeGeneSetCollections | Hypergeometric tests and Gene Set Enrichment Analyses over a list of gene set collections |
annotationConvertor | Convert between different types of gene identifiers |
appendGSTerms | Append gene set terms to GSCA results |
appendGSTerms-method | Append gene set terms to GSCA results |
biogridDataDownload | Download and extract a network interaction matrix from a BioGRID data set |
Biogrid_DM_Interactome | A Sample data set of the package HTSanalyzeR |
Biogrid_DM_Mat | A Sample data set of the package HTSanalyzeR |
celAnnotationConvertor | Convert between different types of gene identifiers for Caenorhabditis Elegans |
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 a collection (list) of gene sets |
drosoAnnotationConvertor | Convert between different types of gene identifiers for Drosophila Melanogaster |
duplicateRemover | Remove duplicates in a named vector of phenotypes |
FDRcollectionGsea | Compute the GSEA false discovery rates for a collection (list) of gene sets |
getTopGeneSets | Select top significant gene sets from GSEA results |
getTopGeneSets-method | Select top significant gene sets from GSEA results |
GOGeneSets | Create a list of gene sets based on GO terms |
GSCA | An S4 class for Gene Set Collection Analyses on high-throughput screens |
GSCA-class | An S4 class for Gene Set Collection Analyses on high-throughput screens |
gseaPlots | Plot GSEA results for one gene set |
gseaScores | Compute enrichment scores for GSEA (Gene Set Enrichment Analysis) |
gseaScoresBatch | Compute enrichment scores for GSEA (Gene Set Enrichment Analysis) |
gseaScoresBatchParallel | Compute enrichment scores for GSEA (Gene Set Enrichment Analysis) |
HTSanalyzeR | HTSanalyzeR Package Overview |
HTSanalyzeR4cellHTS2 | An analysis pipeline for cellHTS2 objects |
hyperGeoTest | Performs hypergeometric tests for over-representation analysis |
interactome | Create an interactome from BioGRID data sets |
interactome-method | Create an interactome from BioGRID data sets |
KcViab_Data4Enrich | A Sample data set of the package HTSanalyzeR |
KcViab_GSCA | A Sample data set of the package HTSanalyzeR |
KcViab_Norm | A Sample data set of the package HTSanalyzeR |
KcViab_NWA | A Sample data set of the package HTSanalyzeR |
KcViab_PVals | A Sample data set of the package HTSanalyzeR |
KeggGeneSets | Create a list of gene sets based on KEGG pathways terms |
mammalAnnotationConvertor | Convert between different types of identifiers for mammalian species |
multiHyperGeoTest | Hypergeometric tests on a list of gene sets |
networkAnalysis | Identify enriched subnetworks |
networkPlot | Plot the enriched subnetwork |
NWA | An S4 class for NetWork Analysis on high-throughput screens |
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 sets on a pair of phenotypes |
permutationPvalueCollectionGsea | Compute the GSEA p-values for a list of gene sets |
plotEnrichMap | Plot and save an enrichment map for results of GSEA or hypergeometric tests |
plotEnrichMap-method | Plot and save an enrichment map for results of GSEA or hypergeometric tests |
plotGSEA | Plot and save figures of GSEA results for top significant gene sets |
plotGSEA-method | Plot and save figures of GSEA results for top significant gene sets |
plotSubNet | Plot and save a figure of the enriched subnetwork |
plotSubNet-method | Plot and save a figure of the enriched subnetwork |
preprocess | A preprocessing method for objects of class GSCA or NWA |
preprocess-method | A preprocessing method for objects of class GSCA or NWA |
report | Write HTML reports for enrichment or network analyses |
report-method | Write HTML reports for enrichment or network analyses |
reportAll | Write HTML reports for both the enrichment and network analyses |
reportAll-method | Write HTML reports for both the enrichment and network analyses |
show | Print summary information for an object of class GSCA or NWA |
show-method | Print summary information for an object of class GSCA or NWA |
summarize | Print summary information for an object of class GSCA or NWA |
summarize-method | Print summary information for an object of class GSCA or NWA |
viewEnrichMap | Plot a figure of the enrichment map for GSEA or Hypergeometric tests |
viewEnrichMap-method | Plot a figure of the enrichment map for GSEA or Hypergeometric tests |
viewGSEA | Plot a figure of GSEA results for one gene set |
viewGSEA-method | Plot a figure of GSEA results for one gene set |
viewSubNet | Plot a figure of the enriched subnetwork |
viewSubNet-method | Plot a figure of the enriched subnetwork |
writeHits | An S4 class for Gene Set Collection Analyses on high-throughput screens |
writeHits-method | An S4 class for Gene Set Collection Analyses on high-throughput screens |
writeReportHTSA | Write HTML reports for enrichment and/or network analyses |