| $,MotifEnrichmentReport-method |
Man page
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| $,MotifEnrichmentResults-method |
Man page
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| $,PWM-method |
Man page
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| $,PWMCutoffBackground-method |
Man page
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| $,PWMEmpiricalBackground-method |
Man page
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| $,PWMGEVBackground-method |
Man page
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| $,PWMLognBackground-method |
Man page
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| .inputPFMfromMatrixOrPWM |
Man page
Source code
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| .inputParamMotifs |
Man page
Source code
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| .inputParamSequences |
Man page
Source code
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| .normalize.bg.seq |
Man page
Source code
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| .normargPfm |
Man page
Source code
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| .normargPriorParams |
Man page
Source code
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| DNAStringSetToList |
Man page
Source code
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| MotifEnrichmentReport-class |
Man page
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| MotifEnrichmentResults-class |
Man page
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| PFMtoPWM |
Man page
Source code
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| PWM-class |
Man page
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| PWMCutoffBackground-class |
Man page
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| PWMEmpiricalBackground-class |
Man page
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| PWMEnrich |
Man page
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| PWMEnrich-package |
Man page
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| PWMGEVBackground-class |
Man page
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| PWMLognBackground-class |
Man page
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| PWMUnscaled |
Man page
Source code
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| [,MotifEnrichmentReport-method |
Man page
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| [,PWMCutoffBackground-method |
Man page
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| [,PWMEmpiricalBackground-method |
Man page
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| [,PWMGEVBackground-method |
Man page
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| [,PWMLognBackground-method |
Man page
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| addLetter |
Source code
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| affinitySequenceSet |
Man page
Source code
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| as.data.frame |
Man page
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| as.data.frame,MotifEnrichmentReport-method |
Man page
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| cloverPvalue1seq |
Man page
Source code
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| cloverScore |
Man page
Source code
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| colMedians |
Man page
Source code
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| colSds |
Man page
Source code
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| concatenateSequences |
Man page
Source code
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| cutoffZscore |
Man page
Source code
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| cutoffZscoreSequenceSet |
Man page
Source code
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| divideRows |
Man page
Source code
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| empiricalPvalue |
Man page
Source code
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| empiricalPvalueSequenceSet |
Man page
Source code
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| getBackgroundFrequencies |
Man page
Source code
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| getPromoters |
Man page
Source code
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| gevPerSequence |
Man page
Source code
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| groupReport |
Man page
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| groupReport,MotifEnrichmentResults-method |
Man page
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| keepFinite |
Man page
Source code
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| length,PWM-method |
Man page
|
| letterA |
Source code
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| letterC |
Source code
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| letterG |
Source code
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| letterT |
Source code
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| logNormPval |
Man page
Source code
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| logNormPvalSequenceSet |
Man page
Source code
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| makeBackground |
Man page
Source code
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| makePWMCutoffBackground |
Man page
Source code
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| makePWMEmpiricalBackground |
Man page
Source code
|
| makePWMGEVBackground |
Man page
Source code
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| makePWMLognBackground |
Man page
Source code
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| makePWMPvalCutoffBackground |
Man page
Source code
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| makePWMPvalCutoffBackgroundFromSeq |
Man page
Source code
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| makePriors |
Man page
Source code
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| makeStartEndPos |
Man page
Source code
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| matrixShuffleZscorePerSequence |
Man page
Source code
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| maxAligned |
Man page
Source code
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| motifDiffEnrichment |
Man page
Source code
|
| motifEcdf |
Man page
Source code
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| motifEnrichment |
Man page
Source code
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| motifIC |
Man page
Source code
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| motifPrAUC |
Man page
Source code
|
| motifRankingForGroup |
Man page
|
| motifRankingForGroup,MotifEnrichmentResults-method |
Man page
|
| motifRankingForSequence |
Man page
|
| motifRankingForSequence,MotifEnrichmentResults-method |
Man page
|
| motifRecoveryAUC |
Man page
Source code
|
| motifScores |
Man page
Source code
|
| motifScoresBigMemory |
Man page
Source code
|
| motifSimilarity |
Man page
Source code
|
| names,MotifEnrichmentReport |
Man page
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| names,MotifEnrichmentReport-method |
Man page
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| names,MotifEnrichmentResults |
Man page
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| names,MotifEnrichmentResults-method |
Man page
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| names,PWM |
Man page
|
| names,PWM-method |
Man page
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| names,PWMCutoffBackground |
Man page
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| names,PWMCutoffBackground-method |
Man page
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| names,PWMEmpiricalBackground |
Man page
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| names,PWMEmpiricalBackground-method |
Man page
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| names,PWMGEVBackground |
Man page
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| names,PWMGEVBackground-method |
Man page
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| names,PWMLognBackground |
Man page
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| names,PWMLognBackground-method |
Man page
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| plot,MotifEnrichmentReport,missing-method |
Man page
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| plot,PWM,missing-method |
Man page
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| plotMotifScores |
Man page
Source code
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| plotMultipleMotifs |
Man page
Source code
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| plotPFM |
Man page
Source code
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| plotTopMotifsGroup |
Man page
|
| plotTopMotifsGroup,MotifEnrichmentResults-method |
Man page
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| plotTopMotifsSequence |
Man page
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| plotTopMotifsSequence,MotifEnrichmentResults-method |
Man page
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| pwm2cons |
Source code
|
| pwm2ic |
Source code
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| rankingProcessAndReturn |
Man page
Source code
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| readJASPAR |
Man page
Source code
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| readMotifs |
Man page
Source code
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| readTRANSFAC |
Man page
Source code
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| registerCoresPWMEnrich |
Man page
Source code
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| reverseComplement,PWM-method |
Man page
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| scanWithPWM |
Man page
Source code
|
| seqLogoGrid |
Man page
Source code
|
| sequenceReport |
Man page
|
| sequenceReport,MotifEnrichmentResults-method |
Man page
|
| show,MotifEnrichmentReport-method |
Man page
|
| show,MotifEnrichmentResults-method |
Man page
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| show,PWM-method |
Man page
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| show,PWMCutoffBackground-method |
Man page
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| show,PWMEmpiricalBackground-method |
Man page
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| show,PWMGEVBackground-method |
Man page
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| show,PWMLognBackground-method |
Man page
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| toPWM |
Man page
Source code
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| tryAllMotifAlignments |
Man page
Source code
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| useBigMemoryPWMEnrich |
Man page
Source code
|
