API for ToPASeq
Topology-based pathway analysis of RNA-seq data
| Global functions | |
|---|---|
| .CePaORA | Source code |
| .CePaSingle | Source code |
| .CePaWeights | Source code |
| .CheckNames | Source code |
| .PRSSingle | Source code |
| .PRSSingle2 | Source code |
| .PRSweights | Source code |
| .PWEASingle | Source code |
| .PWEAscore | Source code |
| .SPIA4plot | Source code |
| .SPIASingle | Source code |
| .SPIAweights | Source code |
| .TIF | Source code |
| .applyTh | Source code |
| .bigPaths | Source code |
| .calculatePCI | Source code |
| .checkDEandAll | Source code |
| .chooseVariance | Source code |
| .cliqueMeanTest | Source code |
| .cliqueVarianceTest | Source code |
| .collectWeightsPRS | Source code |
| .collectWeightsSPIA | Source code |
| .commonGenes | Source code |
| .dagOnly | Source code |
| .degraph | Source code |
| .drawSPIA | Source code |
| .edLi | Source code |
| .estimateCov | Source code |
| .estimateScaledCov | Source code |
| .estimateShrinkedCov | Source code |
| .extractsubset | Source code |
| .fewEdges | Source code |
| .filterSPIA | Source code |
| .finalizeData | Source code |
| .getConnectedComponentList | Source code |
| .getdatp | Source code |
| .graph.T2.test | Source code |
| .graphCov | Source code |
| .hote_mean | Source code |
| .hote_mean_paired | Source code |
| .hotellingIPF | Source code |
| .laplacianFromA | Source code |
| .nodes | Source code |
| .normalizationTAPPA | Source code |
| .notPTIF | Source code |
| .parDE | Source code |
| .parsePerms | Source code |
| .pathwayMeanTest | Source code |
| .pathwayVarianceTest | Source code |
| .prepareData | Source code |
| .preparePathways | Source code |
| .preparePerms | Source code |
| .preparePermsCePap | Source code |
| .preparePermsPWEA | Source code |
| .prepareTIF | Source code |
| .processDEGraph | Source code |
| .processMA | Source code |
| .processRNAseq | Source code |
| .prs | Source code |
| .pwea | Source code |
| .spia | Source code |
| .subsetCov | Source code |
| .tappa | Source code |
| .tappaSingle | Source code |
| .testCliques | Source code |
| .testMA | Source code |
| .testOneConnectedComponent | Source code |
| .testRNAseq | Source code |
| .topologyGSA | Source code |
| .transformPathway | Source code |
| .varianceTest | Source code |
| CePa | Man page Source code |
| DEGraph | Man page Source code |
| PRS_wrapper | Man page Source code |
| PWEA | Man page Source code |
| SPIA | Man page Source code |
| TAPPA | Man page Source code |
| TopologyGSA | Man page Source code |
| accCpp | Source code |
| adjustAttr | Source code |
| adjustAttrCli | Source code |
| applyReduction | Source code |
| betweenness | Source code |
| clipper | Man page Source code |
| colMax | Source code |
| colMin | Source code |
| convertIdentifiersByVector | Man page |
| degtable | Man page Source code |
| degtable.topResult | Man page Source code |
| downstreamCpp | Source code |
| drawGraph | Source code |
| drawNodesPies2 | Source code |
| edgetypeslegend | Source code |
| estimateCF | Source code |
| headline | Source code |
| makeBreaks | Source code |
| makeEdgeList | Source code |
| makeLegend | Source code |
| makeNodeSizeLegend | Source code |
| makeNodeTable | Source code |
| plot.topResult | Source code |
| plotCliques | Source code |
| print.topResult | Source code |
| prs | Man page Source code |
| prsWeights | Man page Source code |
| renderOrig | Source code |
| renderReduced | Source code |
| res | Man page Source code |
| res.topResult | Man page Source code |
| shadowtext | Source code |
| testDESeq2 | Source code |
| testDESeq2perm | Source code |
| testOneGraph | Source code |
| testedgeR | Source code |
| testvoomlimma | Source code |
| testvstlimma | Source code |
| text.lines | Source code |
| topo.sig | Man page Source code |
| topo.sig.topResult | Man page Source code |
