Files in PWMEnrich
PWM enrichment analysis
.Rinstignore
NAMESPACE
DESCRIPTION
build/vignette.rds
R/AllDataClasses.R
R/seqLogoSupp.R
R/misc.R
R/AllGenerics.R
R/diff.R
R/PWM-methods.R
R/PWMBackground-methods.R
R/options.R
R/plot.R
R/readData.R
R/background.R
R/pwm.R
R/similarity.R
R/clover.R
R/MotifEnrichmentResults-methods.R
R/PWMEnrich-package.R
R/MotifEnrichmentReport-methods.R
vignettes/PWMEnrich.Rnw
vignettes/references.bib
man/PWMCutoffBackground-class.Rd
man/groupReport-MotifEnrichmentResults-method.Rd
man/MotifEnrichmentResults-class.Rd
man/operators-PWMEmpiricalBackground.Rd
man/affinitySequenceSet.Rd
man/makePWMLognBackground.Rd
man/toPWM.Rd
man/maxAligned.Rd
man/makeStartEndPos.Rd
man/gevPerSequence.Rd
man/plotMultipleMotifs.Rd
man/dot-inputPFMfromMatrixOrPWM.Rd
man/motifRankingForGroup-MotifEnrichmentResults-method.Rd
man/logNormPval.Rd
man/operators-PWMCutoffBackground.Rd
man/makePriors.Rd
man/show-PWMLognBackground-method.Rd
man/readJASPAR.Rd
man/divideRows.Rd
man/dot-normalize.bg.seq.Rd
man/empiricalPvalueSequenceSet.Rd
man/motifDiffEnrichment.Rd
man/subsetting-PWMEmpiricalBackground.Rd
man/concatenateSequences.Rd
man/motifScores.Rd
man/operators-PWM.Rd
man/PWMLognBackground-class.Rd
man/cutoffZscore.Rd
man/operators-MotifEnrichmentResults.Rd
man/subsetting-PWMGEVBackground.Rd
man/MotifEnrichmentReport-class.Rd
man/operators-PWMLognBackground.Rd
man/keepFinite.Rd
man/PWM-class.Rd
man/subsetting-PWMLognBackground.Rd
man/dot-inputParamMotifs.Rd
man/matrixShuffleZscorePerSequence.Rd
man/PWMUnscaled.Rd
man/makePWMEmpiricalBackground.Rd
man/motifIC.Rd
man/makeBackground.Rd
man/PWMGEVBackground-class.Rd
man/scanWithPWM.Rd
man/operators-MotifEnrichmentReport.Rd
man/plotTopMotifsSequence-MotifEnrichmentResults-method.Rd
man/motifRankingForSequence-MotifEnrichmentResults-method.Rd
man/makePWMPvalCutoffBackgroundFromSeq.Rd
man/motifEcdf.Rd
man/motifEnrichment.Rd
man/makePWMGEVBackground.Rd
man/getBackgroundFrequencies.Rd
man/sequenceReport-MotifEnrichmentResults-method.Rd
man/show-PWMCutoffBackground-method.Rd
man/plotTopMotifsGroup-MotifEnrichmentResults-method.Rd
man/makePWMPvalCutoffBackground.Rd
man/cloverPvalue1seq.Rd
man/subsetting-PWMCutoffBackground.Rd
man/dot-normargPriorParams.Rd
man/readTRANSFAC.Rd
man/motifRecoveryAUC.Rd
man/PWMEmpiricalBackground-class.Rd
man/show-PWMEmpiricalBackground-method.Rd
man/makePWMCutoffBackground.Rd
man/dot-normargPfm.Rd
man/show-PWMGEVBackground-method.Rd
man/colMedians.Rd
man/PWMEnrich-package.Rd
man/motifPrAUC.Rd
man/getPromoters.Rd
man/empiricalPvalue.Rd
man/tryAllMotifAlignments.Rd
man/show-PWM-method.Rd
man/dot-inputParamSequences.Rd
man/useBigMemoryPWMEnrich.Rd
man/plot-MotifEnrichmentReport-missing-method.Rd
man/rankingProcessAndReturn.Rd
man/motifScoresBigMemory.Rd
man/seqLogoGrid.Rd
man/readMotifs.Rd
man/cloverScore.Rd
man/colSds.Rd
man/plotPFM.Rd
man/motifSimilarity.Rd
man/reverseComplement-PWM-method.Rd
man/plotMotifScores.Rd
man/DNAStringSetToList.Rd
man/show-MotifEnrichmentReport-method.Rd
man/registerCoresPWMEnrich.Rd
man/cutoffZscoreSequenceSet.Rd
man/PFMtoPWM.Rd
man/operators-PWMGEVBackground.Rd
man/logNormPvalSequenceSet.Rd
man/plot-PWM-missing-method.Rd
man/as.data.frame-MotifEnrichmentReport-method.Rd
man/show-MotifEnrichmentResults-method.Rd
tests/test-all.R
inst/NEWS
inst/doc/PWMEnrich.Rnw
inst/doc/PWMEnrich.pdf
inst/doc/PWMEnrich.R
inst/extdata/tinman-early-top20.fa
inst/extdata/example.fa
inst/extdata/jaspar-insecta.jaspar
inst/extdata/pfm_vertebrates.txt
inst/extdata/bg.seq-test.RData
inst/extdata/stripe2.fa
inst/extdata/example.transfac
inst/tests/test_similarity.R
inst/tests/test_motifEnrichment.R
inst/tests/test_invalidInput.R
inst/tests/test_clover.R
