API for RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
| Global functions | |
|---|---|
| .alpha.adjust | Source code |
| .annotate.regulons.gsea2 | Source code |
| .annotate.regulons.hypergeo | Source code |
| .annotate.regulons.jaccard | Source code |
| .annotate.samples.gsea | Source code |
| .avs.checks | Source code |
| .barplot.pos.vs.neg | Source code |
| .bcpower | Source code |
| .boxcox.adj | Source code |
| .edf.pos.vs.neg | Source code |
| .estimate.bcpower | Source code |
| .expDataChecks | Source code |
| .fgseaScores4TNI | Source code |
| .get.regulon.summary | Source code |
| .get.tnet.summary | Source code |
| .gmm.scores | Source code |
| .gmmlist | Source code |
| .gsea2.target.contribution | Source code |
| .hclust2igraph | Source code |
| .hyperGeoTest4RTN | Source code |
| .hypergeo.genesets | Source code |
| .isUnloggedData | Source code |
| .jaccard.genesets | Source code |
| .log2transform | Source code |
| .mi2gmm.dpi | Source code |
| .mi2gmm.ref | Source code |
| .mtdata | Source code |
| .perm.pmin.pooled | Source code |
| .perm.pmin.separate | Source code |
| .points.pos.vs.neg | Source code |
| .preprocess.genesets | Source code |
| .regulon.summary | Source code |
| .regulonCounts | Source code |
| .regulonGroupFET | Source code |
| .run.tni.gsea1.alternative | Source code |
| .run.tni.gsea2.alternative | Source code |
| .target.contribution | Source code |
| .tni.stratification.area | Source code |
| .tni.stratification.gsea2 | Source code |
| .update_pEVSE | Source code |
| AVS-class | Man page |
| RTN | Man page |
| RTN-package | Man page |
| TNA-class | Man page |
| TNI-class | Man page |
| all.binaryValues | Source code |
| all.characterValues | Source code |
| all.integerValues | Source code |
| avs.evse | Man page |
| avs.evse,AVS-method | Man page |
| avs.get | Man page |
| avs.get,AVS-method | Man page |
| avs.pevse | Man page |
| avs.pevse,AVS-method | Man page |
| avs.plot1 | Man page Source code |
| avs.plot2 | Man page Source code |
| avs.vse | Man page |
| avs.vse,AVS-method | Man page |
| avsplot1 | Source code |
| avsplot2 | Source code |
| cdt.list | Source code |
| cdt.stability | Source code |
| cdt.table | Source code |
| check.format1 | Source code |
| check.format2 | Source code |
| checkModuationEffect | Source code |
| checkTars | Source code |
| cv.filter | Source code |
| data.integration | Source code |
| eqtlExtract | Source code |
| eqtlExtractAnova | Source code |
| eqtlExtractFull | Source code |
| eqtlTest | Source code |
| eqtlTestDetailed | Source code |
| eqtlTestDetailedAnova | Source code |
| evsea | Source code |
| evseaproxy | Source code |
| expressionCorrelation | Source code |
| get.avsdist | Source code |
| get.eqtldist | Source code |
| get.merged.data1 | Source code |
| get.merged.data2 | Source code |
| get.pre_eqtldist | Source code |
| getAnnotOverlap1 | Source code |
| getAnnotOverlap2 | Source code |
| getAnnotRanges | Source code |
| getAvsRanges | Source code |
| getEvseEqtls | Source code |
| getEvseMatrix | Source code |
| getMappedClusters | Source code |
| getMappedMarkers | Source code |
| getMarkers.rset | Source code |
| getMarkers.vset | Source code |
| getRandomAvsRanges | Source code |
| getUniverseCounts1 | Source code |
| getUniverseCounts2 | Source code |
| gettfs | Source code |
| gsea1tna | Source code |
| gsea2tna | Source code |
| gseaScores4RTN | Source code |
| gseaScoresBatch4RTN | Source code |
| gsplot1 | Source code |
| gsplot2 | Source code |
| hcEdges.filter | Source code |
| hclust2igraph | Source code |
| hits.preprocess | Source code |
| hyperGeoTest4RTN | Source code |
| is.color | Source code |
| is.singleInteger | Source code |
| is.singleLogical | Source code |
| is.singleNumber | Source code |
| is.singleString | Source code |
| isParallel | Source code |
| make.plot1 | Source code |
| make.plot2 | Source code |
| maprset | Source code |
| mapvset | Source code |
| miMdTfStats | Source code |
| miThresholdMd | Source code |
| miThresholdMdTf | Source code |
| mutualInformation | Source code |
| p.adjust.cdt.list | Source code |
| p.adjust.cdt.table | Source code |
| p.format.cdt.table | Source code |
| pheno.preprocess | Source code |
| pksData | Man page |
| plot.gsea1 | Source code |
| plot.gsea2 | Source code |
| pre_evsea | Source code |
| report.vset | Source code |
| run.gsea1 | Source code |
| run.gsea2 | Source code |
| setregs1 | Source code |
| setregs2 | Source code |
| shtest | Source code |
| sortAnnotation | Source code |
| sortblock.cdt.list | Source code |
| stni | Man page |
| tfsData | Man page |
| tna.duplicate.remover | Source code |
| tna.get | Man page |
| tna.get,TNA-method | Man page |
| tna.gsea1 | Man page |
| tna.gsea1,TNA-method | Man page |
| tna.gsea2 | Man page |
| tna.gsea2,TNA-method | Man page |
| tna.mra | Man page |
| tna.mra,TNA-method | Man page |
| tna.perm.pvalues | Source code |
| tna.plot.gsea1 | Man page Source code |
| tna.plot.gsea2 | Man page Source code |
| tna.preprocess | Source code |
| tnaData | Man page |
| tnai.checks | Source code |
| tni.alpha.adjust | Man page Source code |
| tni.amap | Source code |
| tni.annotate.regulons | Man page |
| tni.annotate.regulons,TNI-method | Man page |
| tni.annotate.samples | Man page |
| tni.annotate.samples,TNI-method | Man page |
| tni.area3 | Man page |
| tni.area3,TNI-method | Man page |
| tni.boot | Source code |
| tni.bootstrap | Man page |
| tni.bootstrap,TNI-method | Man page |
| tni.conditional | Man page |
| tni.conditional,TNI-method | Man page |
| tni.constructor | Man page Source code |
| tni.cor | Source code |
| tni.dpi | Source code |
| tni.dpi.filter | Man page |
| tni.dpi.filter,TNI-method | Man page |
| tni.get | Man page |
| tni.get,TNI-method | Man page |
| tni.graph | Man page |
| tni.graph,TNI-method | Man page |
| tni.gsea2 | Man page |
| tni.gsea2,TNI-method | Man page |
| tni.mmap | Source code |
| tni.mmap.detailed | Source code |
| tni.overlap.genesets | Man page |
| tni.overlap.genesets,TNI-method | Man page |
| tni.perm.pooled | Source code |
| tni.perm.separate | Source code |
| tni.permutation | Man page |
| tni.permutation,TNI-method | Man page |
| tni.phyper | Source code |
| tni.plot.checks | Man page Source code |
| tni.plot.sre | Man page Source code |
| tni.pmin | Source code |
| tni.preprocess | Man page |
| tni.preprocess,TNI-method | Man page |
| tni.prune | Man page |
| tni.prune,TNI-method | Man page |
| tni.regulon.summary | Man page |
| tni.regulon.summary,TNI-method | Man page |
| tni.replace.samples | Man page |
| tni.replace.samples,TNI-method | Man page |
| tni.rmap | Source code |
| tni.sre | Man page |
| tni.sre,TNI-method | Man page |
| tni2tna.preprocess | Man page |
| tni2tna.preprocess,TNI-method | Man page |
| tniData | Man page |
| translateQuery | Source code |
| treemap | Source code |
| upgradeTNA | Man page Source code |
| upgradeTNI | Man page Source code |
| vsea | Source code |
| vseformat | Source code |
| vsereport | Source code |
