API for fmicompbio/monaLisa
Binned Motif Enrichment Analysis and Visualization
| Global functions | |
|---|---|
| .assertScalar | Source code |
| .assertVector | Source code |
| .binomEnrichmentTest | Source code |
| .breaksEqualN | Source code |
| .breaksEqualWidth | Source code |
| .calcExpFg | Source code |
| .calcKmerEnrichment | Man page Source code |
| .calcLog2Enr | Source code |
| .calcMotifEnrichment | Man page Source code |
| .calcPearsonResiduals | Source code |
| .calculateGCweight | Man page Source code |
| .checkDfValidity | Man page Source code |
| .checkHomerRun | Source code |
| .checkIfSeqsAreEqualLength | Man page Source code |
| .compareMotifKmer | Source code |
| .compareMotifPair | Source code |
| .cons2matrix | Man page Source code |
| .defineBackground | Man page Source code |
| .dumpPWMsToHomer2File | Source code |
| .filterSeqs | Man page Source code |
| .fisherEnrichmentTest | Source code |
| .glmnetRandomizedLasso | Man page Source code |
| .iterativeNormForKmers | Man page Source code |
| .matchPWM.concat | Source code |
| .normForKmers | Man page Source code |
| .readPWMsFromHomer2File | Source code |
| addLetter | Source code |
| annoSeqlogo | Man page Source code |
| bin | Man page Source code |
| calcBinnedKmerEnr | Man page Source code |
| calcBinnedMotifEnrHomer | Man page Source code |
| calcBinnedMotifEnrR | Man page Source code |
| dumpJaspar | Man page Source code |
| findHomer | Man page Source code |
| findMotifHits | Man page |
| findMotifHits,PWMatrix,DNAString-method | Man page |
| findMotifHits,PWMatrix,DNAStringSet-method | Man page |
| findMotifHits,PWMatrix,GRanges-method | Man page |
| findMotifHits,PWMatrix,character-method | Man page |
| findMotifHits,PWMatrixList,DNAString-method | Man page |
| findMotifHits,PWMatrixList,DNAStringSet-method | Man page |
| findMotifHits,PWMatrixList,GRanges-method | Man page |
| findMotifHits,PWMatrixList,character-method | Man page |
| findMotifHits,character,DNAString-method | Man page |
| findMotifHits,character,DNAStringSet-method | Man page |
| findMotifHits,character,character-method | Man page |
| getColsByBin | Man page Source code |
| getKmerFreq | Man page Source code |
| getSetZeroBin | Man page |
| getZeroBin | Man page Source code |
| homerToPFMatrixList | Man page Source code |
| letterA | Source code |
| letterC | Source code |
| letterG | Source code |
| letterT | Source code |
| monaLisa | Man page |
| monaLisa-package | Man page |
| motifKmerSimilarity | Man page Source code |
| motifSimilarity | Man page Source code |
| parseHomerOutput | Man page Source code |
| pfm2ic | Source code |
| plotBinDensity | Man page Source code |
| plotBinDiagnostics | Man page Source code |
| plotBinHist | Man page Source code |
| plotBinScatter | Man page Source code |
| plotMotifHeatmaps | Man page Source code |
| plotSelectionProb | Man page Source code |
| plotStabilityPaths | Man page Source code |
| prepareHomer | Man page Source code |
| randLassoStabSel | Man page Source code |
| sampleRandomRegions | Man page Source code |
| seqLogoGrob | Man page Source code |
| setZeroBin | Man page Source code |
