Index

A

add() (gnocis.biomarkers.biomarkers method) addComplements (gnocis.sequences.IID attribute)

addModel (gnocis.models.crossvalidation attribute) addReverseComplements (gnocis.sequences.MarkovChain attribute) annotation (gnocis.sequences.sequence attribute)

B

biomarkers (class in gnocis.biomarkers) (gnocis.biomarkers.biomarkers attribute) bitmask (gnocis.features.kSpectrum attribute) (gnocis.features.kSpectrumGPS attribute) (gnocis.features.kSpectrumMM attribute) (gnocis.features.kSpectrumMMD attribute)

bstr() (gnocis.regions.region method) (gnocis.regions.regions method)

C

c (gnocis.motifs.IUPACMotif attribute) cachedOcc (gnocis.motifs.IUPACMotif attribute) (gnocis.motifs.PWMMotif attribute) cachedSequence (gnocis.features.feature attribute) (gnocis.features.kSpectrum attribute) (gnocis.features.kSpectrumGPS attribute) (gnocis.features.kSpectrumMM attribute) (gnocis.features.kSpectrumMMD attribute) (gnocis.motifs.IUPACMotif attribute) (gnocis.motifs.PWMMotif attribute) cachedSpectrum (gnocis.features.kSpectrum attribute) (gnocis.features.kSpectrumGPS attribute) (gnocis.features.kSpectrumMM attribute) (gnocis.features.kSpectrumMMD attribute)

cachedValue (gnocis.features.feature attribute) calibrate (gnocis.models.crossvalidation attribute) calibrateGenomewidePrecision (gnocis.models.sequenceModel attribute) center() (gnocis.regions.region method) CI() (in module gnocis.common) comparableSpectrum (gnocis.sequences.MarkovChain attribute) cRC (gnocis.motifs.IUPACMotif attribute) createDummyPREdictorModel() (in module gnocis.models) crossvalidate() (in module gnocis.models) crossvalidation (class in gnocis.models) CVModelPredictions (class in gnocis.models)

D

degree (gnocis.sequences.MarkovChain attribute) deltaResize() (gnocis.regions.regions method)

diffsummary() (gnocis.features.features method) distCut (gnocis.features.featurePREdictorMotifPairOccurrenceFrequency attribute) dummy() (gnocis.regions.regions method)

E

end (gnocis.motifs.motifOccurrence attribute) (gnocis.regions.region attribute) enrichmentSpectrum() (gnocis.biomarkers.biomarkers method) exclusion() (gnocis.regions.regions method) expected() (gnocis.regions.regions method)

ext (gnocis.regions.region attribute) extract() (gnocis.regions.regions method) extractSequences() (gnocis.regions.regions method) extractSequencesFrom2bit() (gnocis.regions.regions method) extractSequencesFromFASTA() (gnocis.regions.regions method)

F

feature (class in gnocis.features) (gnocis.features.scaledFeature attribute) (gnocis.regions.region attribute) featureMotifOccurrenceFrequency (class in gnocis.features) featurePREdictorMotifPairOccurrenceFrequency (class in gnocis.features) features (class in gnocis.features) (gnocis.features.features attribute) (gnocis.features.kSpectrum attribute) (gnocis.features.kSpectrumGPS attribute) (gnocis.features.kSpectrumMM attribute) (gnocis.features.kSpectrumMMD attribute)

featureScaler (class in gnocis.features) fetch() (gnocis.sequences.sequenceStream method) filter() (gnocis.regions.regions method) find() (gnocis.motifs.IUPACMotif method) (gnocis.motifs.PWMMotif method) flatten() (gnocis.regions.regions method)

G

generate() (gnocis.sequences.IID method) (gnocis.sequences.MarkovChain method) generateFASTA() (gnocis.sequences.sequenceGenerator method) generateSet() (gnocis.sequences.sequenceGenerator method) generateStream() (gnocis.sequences.sequenceGenerator method) get() (gnocis.features.feature method) (gnocis.features.featureMotifOccurrenceFrequency method) (gnocis.features.featurePREdictorMotifPairOccurrenceFrequency method) (gnocis.features.kSpectrumFeatureGPS method) (gnocis.features.kSpectrumMMDFeature method) (gnocis.features.scaledFeature method) getAll() (gnocis.features.features method) (gnocis.features.featureScaler method) getAUC() (in module gnocis.validation) getAUCTable (gnocis.models.crossvalidation attribute) getConfigurationTable (gnocis.models.crossvalidation attribute) getConfusionMatrix (gnocis.models.sequenceModel attribute) getConfusionMatrix() (in module gnocis.validation) getConfusionMatrixStatistics() (in module gnocis.validation) getEValueThreshold() (gnocis.motifs.PWMMotif method) getFloat() (in module gnocis.common) getOptimalAccuracyThreshold (gnocis.models.sequenceModel attribute) getPRC (gnocis.models.sequenceModel attribute) getPRC() (in module gnocis.validation) getPRCAUC (gnocis.models.sequenceModel attribute) getPrecisionThreshold (gnocis.models.sequenceModel attribute) getReverseComplementaryDNASequence() (in module gnocis.common) getROC (gnocis.models.sequenceModel attribute) getROC() (in module gnocis.validation) getROCAUC (gnocis.models.sequenceModel attribute)

getSequenceFeatureVector() (gnocis.sklearnModels.sequenceModelLasso method) (gnocis.sklearnModels.sequenceModelRF method) (gnocis.sklearnModels.sequenceModelSVM method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadratic method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadraticAutoScale method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadraticCUDA method) getSequenceScores (gnocis.models.sequenceModel attribute) getSequenceStreamFromPath() (in module gnocis.sequences) getSequenceWindowRegions() (in module gnocis.sequences) getStatTable (gnocis.models.CVModelPredictions attribute) getTrainer (gnocis.models.sequenceModelDummy attribute) (gnocis.models.sequenceModelLogOdds attribute) getTrainer() (gnocis.sklearnModels.sequenceModelLasso method) (gnocis.sklearnModels.sequenceModelRF method) (gnocis.sklearnModels.sequenceModelSVM method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadratic method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadraticAutoScale method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadraticCUDA method) getValidationStatistics (gnocis.models.sequenceModel attribute) gnocis.biomarkers (module) gnocis.common (module) gnocis.features (module) gnocis.models (module) gnocis.motifs (module) gnocis.regions (module) gnocis.sequences (module) gnocis.sklearnModels (module) gnocis.sklearnModelsOpt (module) gnocis.validation (module) group (gnocis.regions.region attribute)

H

HBMEs() (gnocis.biomarkers.biomarkers method)

I

IID (class in gnocis.sequences) index (gnocis.features.kSpectrumFeatureGPS attribute) (gnocis.features.kSpectrumMMDFeature attribute)

initialDistribution (gnocis.sequences.MarkovChain attribute) intersection() (gnocis.regions.regions method) IUPACMotif (class in gnocis.motifs)

K

KLdiv() (in module gnocis.common) kmer (gnocis.features.kSpectrumFeatureGPS attribute) (gnocis.features.kSpectrumMMDFeature attribute) kmerByIndex (gnocis.features.kSpectrum attribute) (gnocis.features.kSpectrumGPS attribute) (gnocis.features.kSpectrumMM attribute) (gnocis.features.kSpectrumMMD attribute) kSpectrum (class in gnocis.features)

kSpectrum() (gnocis.features.features static method) kSpectrumFeatureGPS (class in gnocis.features) kSpectrumGPS (class in gnocis.features) kSpectrumGPS() (gnocis.features.features static method) kSpectrumMM (class in gnocis.features) kSpectrumMM() (gnocis.features.features static method) kSpectrumMMD (class in gnocis.features) kSpectrumMMD() (gnocis.features.features static method) kSpectrumMMDFeature (class in gnocis.features)

L

label (gnocis.validation.validationPair attribute) label() (gnocis.sequences.sequence method) (gnocis.sequences.sequences method) labels (gnocis.sequences.sequence attribute) labels() (gnocis.sequences.sequences method) LBMEs() (gnocis.biomarkers.biomarkers method) loadBED() (in module gnocis.regions)

loadBEDGZ() (in module gnocis.regions) loadCoordinateList() (in module gnocis.regions) loadFASTA() (in module gnocis.sequences) loadFASTAGZ() (in module gnocis.sequences) loadGFF() (in module gnocis.regions) loadGFFGZ() (in module gnocis.regions) loadMEMEPWMDatabase() (in module gnocis.motifs)

M

m (gnocis.features.featureMotifOccurrenceFrequency attribute) mA (gnocis.features.featurePREdictorMotifPairOccurrenceFrequency attribute) markers (gnocis.regions.region attribute) MarkovChain (class in gnocis.sequences) mB (gnocis.features.featurePREdictorMotifPairOccurrenceFrequency attribute) mean() (in module gnocis.common) merge() (gnocis.regions.regions method)

motif (gnocis.motifs.IUPACMotif attribute) (gnocis.motifs.motifOccurrence attribute) motifOccurrence (class in gnocis.motifs) motifPairSpectrum() (gnocis.features.features static method) motifs (class in gnocis.motifs) (gnocis.motifs.motifs attribute) motifSpectrum() (gnocis.features.features static method)

N

name (gnocis.biomarkers.biomarkers attribute) (gnocis.features.features attribute) (gnocis.motifs.IUPACMotif attribute) (gnocis.motifs.PWMMotif attribute) (gnocis.motifs.motifs attribute) (gnocis.regions.regions attribute) (gnocis.sequences.sequence attribute) (gnocis.sequences.sequenceLabel attribute) (gnocis.sequences.sequences attribute) (gnocis.validation.validationPair attribute) negativeThreshold (gnocis.biomarkers.biomarkers attribute) nFeatures (gnocis.features.kSpectrum attribute) (gnocis.features.kSpectrumGPS attribute) (gnocis.features.kSpectrumMM attribute) (gnocis.features.kSpectrumMMD attribute)

nGenerated (gnocis.sequences.IID attribute) (gnocis.sequences.MarkovChain attribute) nkmers (gnocis.features.kSpectrumGPS attribute) nmismatches (gnocis.motifs.IUPACMotif attribute) nonOverlap() (gnocis.regions.regions method) nspectrum (gnocis.features.kSpectrum attribute) (gnocis.features.kSpectrumGPS attribute) (gnocis.features.kSpectrumMM attribute) (gnocis.features.kSpectrumMMD attribute) ntDistribution (gnocis.sequences.IID attribute) nucleotidePrecision() (gnocis.regions.regions method) nucleotidePrecisionBarplot() (in module gnocis.regions) nucleotideRegionF1Barplot() (in module gnocis.regions) nvalues (gnocis.features.features attribute)

O

occFreq (gnocis.motifs.motifs attribute) overlap() (gnocis.regions.regions method) overlapPrecision() (gnocis.regions.regions method)

overlapPrecisionBarplot() (in module gnocis.regions) overlapSensitivity() (gnocis.regions.regions method) overlapSensitivityBarplot() (in module gnocis.regions)

P

pairFreq (gnocis.motifs.motifs attribute) parent (gnocis.features.kSpectrumFeatureGPS attribute) (gnocis.features.kSpectrumMMDFeature attribute) path (gnocis.motifs.PWMMotif attribute) (gnocis.sequences.sequence attribute) plotPRC (gnocis.models.crossvalidation attribute) (gnocis.models.sequenceModel attribute) plotROC (gnocis.models.crossvalidation attribute) point2D (class in gnocis.validation) positiveThreshold (gnocis.biomarkers.biomarkers attribute) predict (gnocis.models.crossvalidation attribute) (gnocis.models.sequenceModel attribute) predictCore (gnocis.models.CVModelPredictions attribute) (gnocis.models.sequenceModel attribute)

predictionBarplot() (in module gnocis.regions) predictSequenceStreamCurves (gnocis.models.sequenceModel attribute) predictSequenceStreamRegions (gnocis.models.sequenceModel attribute) prepared (gnocis.sequences.IID attribute) (gnocis.sequences.MarkovChain attribute) printStatistics() (gnocis.regions.regions method) (gnocis.sequences.sequences method) printTestStatistics (gnocis.models.sequenceModel attribute) printValidationStatistics() (in module gnocis.validation) probspectrum (gnocis.sequences.MarkovChain attribute) pseudoCounts (gnocis.sequences.IID attribute) (gnocis.sequences.MarkovChain attribute) PWMF (gnocis.motifs.PWMMotif attribute) PWMMotif (class in gnocis.motifs) PWMRC (gnocis.motifs.PWMMotif attribute)

R

randomSplit() (gnocis.regions.regions method) (gnocis.sequences.sequences method) rank (gnocis.validation.point2D attribute) recenter() (gnocis.regions.regions method) regexMotif (gnocis.motifs.IUPACMotif attribute) regexMotifRC (gnocis.motifs.IUPACMotif attribute) region (class in gnocis.regions) regionBarplot() (in module gnocis.regions)

regions (class in gnocis.regions) (gnocis.models.CVModelPredictions attribute) (gnocis.regions.regions attribute) rename() (gnocis.regions.regions method) (gnocis.sequences.sequences method) RF (class in gnocis.sklearnModels) Ringrose2003 (gnocis.motifs.motifs attribute) Ringrose2003GTGT (gnocis.motifs.motifs attribute)

S

sample() (gnocis.regions.regions method) (gnocis.sequences.sequences method) saveBED() (gnocis.regions.regions method) saveCoordinateList() (gnocis.regions.regions method) saveFASTA() (gnocis.sequences.sequences method) saveGFF() (gnocis.regions.regions method) scale() (gnocis.features.features method) scaledFeature (class in gnocis.features) score (gnocis.models.sequenceModel attribute) (gnocis.regions.region attribute) (gnocis.validation.validationPair attribute) score() (gnocis.sklearnModels.RF method) (gnocis.sklearnModels.SVM method) scoreSequence (gnocis.models.sequenceModel attribute) scoreWindow (gnocis.models.sequenceModelDummy attribute) (gnocis.models.sequenceModelLogOdds attribute) scoreWindow() (gnocis.sklearnModels.sequenceModelLasso method) (gnocis.sklearnModels.sequenceModelRF method) (gnocis.sklearnModels.sequenceModelSVM method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadratic method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadraticAutoScale method) (gnocis.sklearnModelsOpt.sequenceModelSVMOptimizedQuadraticCUDA method) SE() (in module gnocis.common) section (gnocis.features.kSpectrumFeatureGPS attribute) seq (gnocis.motifs.motifOccurrence attribute) (gnocis.regions.region attribute) (gnocis.sequences.sequence attribute) sequence (class in gnocis.sequences) sequenceGenerator (class in gnocis.sequences) sequenceLabel (class in gnocis.sequences) sequenceLengths() (gnocis.sequences.sequences method) (gnocis.sequences.sequenceStream method) sequenceModel (class in gnocis.models) sequenceModelDummy (class in gnocis.models) sequenceModelLasso (class in gnocis.sklearnModels) sequenceModelLogOdds (class in gnocis.models)

sequenceModelRF (class in gnocis.sklearnModels) sequenceModelSVM (class in gnocis.sklearnModels) sequenceModelSVMOptimizedQuadratic (class in gnocis.sklearnModelsOpt) sequenceModelSVMOptimizedQuadraticAutoScale (class in gnocis.sklearnModelsOpt) sequenceModelSVMOptimizedQuadraticCUDA (class in gnocis.sklearnModelsOpt) sequences (class in gnocis.sequences) (gnocis.sequences.sequences attribute) sequenceStream (class in gnocis.sequences) sequenceStream2bit (class in gnocis.sequences) sequenceStreamFASTA (class in gnocis.sequences) setConfidenceIntervalFunction() (in module gnocis.common) setCorePredictions (gnocis.models.CVModelPredictions attribute) setNCores() (in module gnocis.models) setNThreadFetch() (in module gnocis.models) setPWM() (gnocis.motifs.PWMMotif method) setSeed() (in module gnocis.common) singleton() (gnocis.regions.region method) sort() (gnocis.regions.regions method) source (gnocis.regions.region attribute) sourceRegion (gnocis.sequences.sequence attribute) sourceRegions() (gnocis.sequences.sequences method) spectrum (gnocis.sequences.IID attribute) (gnocis.sequences.MarkovChain attribute) split() (gnocis.sequences.sequences method) start (gnocis.motifs.motifOccurrence attribute) (gnocis.regions.region attribute) std() (in module gnocis.common) strand (gnocis.motifs.motifOccurrence attribute) (gnocis.regions.region attribute) stream2bit() (in module gnocis.sequences) streamFASTA() (in module gnocis.sequences) streamFASTAGZ() (in module gnocis.sequences) streamFullSequences() (gnocis.sequences.sequenceStream method) streamSequenceWindows() (in module gnocis.sequences) summary() (gnocis.features.features method) SVM (class in gnocis.sklearnModels)

T

table (gnocis.motifs.motifs attribute) table() (gnocis.features.features method) (gnocis.regions.regions method) (gnocis.sequences.sequences method) threshold (gnocis.motifs.PWMMotif attribute) train (gnocis.models.sequenceModel attribute)

train() (gnocis.sklearnModels.RF method) (gnocis.sklearnModels.SVM method) trainingSequences (gnocis.sequences.IID attribute) (gnocis.sequences.MarkovChain attribute) trainPREdictorModel() (in module gnocis.models) trainSinglePREdictorModel() (in module gnocis.models)

U

useSciPyConfidenceIntervals() (in module gnocis.common)

V

validationPair (class in gnocis.validation) value (gnocis.sequences.sequenceLabel attribute)

values (gnocis.features.features attribute) vScale (gnocis.features.scaledFeature attribute) vSub (gnocis.features.scaledFeature attribute)

W

weights() (gnocis.sklearnModels.RF method) (gnocis.sklearnModels.SVM method) windowRegions() (gnocis.sequences.sequences method) (gnocis.sequences.sequenceStream method)

windows() (gnocis.sequences.sequence method) (gnocis.sequences.sequenceStream method) (gnocis.sequences.sequences method) withLabel() (gnocis.sequences.sequences method)

X

x (gnocis.validation.point2D attribute)

Y

y (gnocis.validation.point2D attribute)