A C D E F G H I K L M O P R S U misc
ALLModules | ISA transcription modules for the ALL data |
ALLModulesSmall | ISA transcription modules for the ALL data |
annotate | Convert ISA modules to a Biclust object, or the opposite |
annotation-method | A set of ISA modules |
anrichment | Enrichment analysis for transcription modules, based on user-defined categories |
CHRListHyperGParams | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
CHRListHyperGParams-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
CHRListHyperGResult | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
CHRListHyperGResult-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
class:ISAModules | A set of ISA modules |
coerce-method | Convert ISA modules to a Biclust object, or the opposite |
condGeneIdUniverse-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
conditional-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
conditional-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
conditional<--method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
condPlot | Plot sample scores of a transcription module |
dim-method | A set of ISA modules |
drive | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
drive-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
drive<- | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
drive<--method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
expectedCounts-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
expPlot | Expression matrix plots for ISA modules |
expPlotColbar | Expression matrix plots for ISA modules |
expPlotCreate | Expression matrix plots for ISA modules |
featExprs | Expression Set, normalized for using with ISA |
featExprs-method | Expression Set, normalized for using with ISA |
featureNames-method | A set of ISA modules |
featureThreshold | A set of ISA modules |
featureThreshold-method | A set of ISA modules |
geneCounts-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
geneIdsByCategory-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
geneIdUniverse-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
geneMappedCount-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
GeneralListHyperGParams | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
GeneralListHyperGParams-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
GeneralListHyperGResult | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
GeneralListHyperGResult-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
getFeatureMatrix | A set of ISA modules |
getFeatureMatrix-method | A set of ISA modules |
getFeatureNames | A set of ISA modules |
getFeatureNames-method | A set of ISA modules |
getFeatures | A set of ISA modules |
getFeatures-method | A set of ISA modules |
getFeatureScores | A set of ISA modules |
getFeatureScores-method | A set of ISA modules |
getFullFeatureMatrix | A set of ISA modules |
getFullFeatureMatrix-method | A set of ISA modules |
getFullSampleMatrix | A set of ISA modules |
getFullSampleMatrix-method | A set of ISA modules |
getNoFeatures | A set of ISA modules |
getNoFeatures-method | A set of ISA modules |
getNoSamples | A set of ISA modules |
getNoSamples-method | A set of ISA modules |
getOrganism | A set of ISA modules |
getOrganism-method | A set of ISA modules |
getSampleMatrix | A set of ISA modules |
getSampleMatrix-method | A set of ISA modules |
getSampleNames | A set of ISA modules |
getSampleNames-method | A set of ISA modules |
getSamples | A set of ISA modules |
getSamples-method | A set of ISA modules |
getSampleScores | A set of ISA modules |
getSampleScores-method | A set of ISA modules |
gograph | Plot part of the Gene Ontology hierarchy |
gographPlot | Plot part of the Gene Ontology hierarchy |
GOListHyperGParams | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
GOListHyperGParams-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
GOListHyperGResult | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
GOListHyperGResult-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
hasNA | Expression Set, normalized for using with ISA |
hasNA-method | Expression Set, normalized for using with ISA |
hasNA<- | Expression Set, normalized for using with ISA |
hasNA<--method | Expression Set, normalized for using with ISA |
htmlReport-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
hyperGTest-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
ISA | Iterative Signature Algorithm on Gene Expression data |
ISA2heatmap | Heatmap of a transcription module |
ISACHR | Calculate chromosome enrichment for transcription modules |
ISAEnrichment | Enrichment analysis for transcription modules, based on user-defined categories |
ISAExpressionSet | Expression Set, normalized for using with ISA |
ISAExpressionSet-class | Expression Set, normalized for using with ISA |
ISAFilterRobust | Robustness of ISA biclusters |
ISAGO | Calculate Gene Ontology enrichment for transcription modules |
ISAHTML | Create HTML summary pages from the result of modular analysis |
ISAHTMLModules | Create HTML summary pages from the result of modular analysis |
ISAHTMLTable | Create HTML summary pages from the result of modular analysis |
ISAIterate | Perform the Iterative Signature Algorithm |
ISAKEGG | Calculate KEGG Pathway enrichment for transcription modules |
ISAmiRNA | Calculate (predicted) miRNA target enrichment for transcription modules |
ISAmnplot | Plot group means against each other, for an ISA module |
ISAModules | A set of ISA modules |
ISAModules-class | A set of ISA modules |
ISANormalize | Normalize expression data for the Iterative Signature Algorithm |
ISARobustness | Robustness of ISA biclusters |
ISASweep | Create an ISA module tree |
ISASweepGraph | Create an ISA module tree |
ISASweepGraphPlot | Create an ISA module tree |
ISAUnique | Remove duplicated ISA modules |
KEGGListHyperGParams | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
KEGGListHyperGParams-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
KEGGListHyperGResult | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
KEGGListHyperGResult-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
length-method | A set of ISA modules |
ListHyperGParams | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
ListHyperGParams-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
ListHyperGResult | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
ListHyperGResult-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
makeValidParams-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
miRNAListHyperGParams | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
miRNAListHyperGParams-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
miRNAListHyperGResult | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
miRNAListHyperGResult-class | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
mnplot | Plot group means against each other, for an ISA module |
oddsRatios-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
ontology-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
ontology-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
ontology<--method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets. |
overlap | Overlap of ISA biclusters |
overlapPlot | Overlap of ISA biclusters |
pData-method | A set of ISA modules |
prenormalized | Expression Set, normalized for using with ISA |
prenormalized-method | Expression Set, normalized for using with ISA |
prenormalized<- | Expression Set, normalized for using with ISA |
prenormalized<--method | Expression Set, normalized for using with ISA |
print.ISAexpPlot | Expression matrix plots for ISA modules |
profilePlot | Profile plots for ISA biclusters |
pvalues-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
runData | A set of ISA modules |
runData-method | A set of ISA modules |
sampExprs | Expression Set, normalized for using with ISA |
sampExprs-method | Expression Set, normalized for using with ISA |
sampleNames-method | A set of ISA modules |
sampleThreshold | A set of ISA modules |
sampleThreshold-method | A set of ISA modules |
seedData | A set of ISA modules |
seedData-method | A set of ISA modules |
sigCategories-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
summary-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
universeCounts-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
universeMappedCount-method | Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets |
[-method | A set of ISA modules |
[[-method | A set of ISA modules |