Man pages for MEET
MEET: Motif Elements Estimation Toolkit

align.clustalwMultiple sequence alignment by means of ClustalW
align.MEMEMultiple sequence alignment by means of MEME.
AlignmentTo line up Transcription Factor Binding Sites through...
align.muscleMultiple sequence alignment by means of Muscle (MUltiple...
BackgroundOrganismMatrix of background frequencies
CalculInformationInformation content in each position of a set of aligned DNA...
CalculPSSMPosition Specific Scoring Matrices from a set of aligned...
CalculPWMCalculPWM: To calculate Position Weight Matrix
CalculRedundancyCalculRedundancy: To calculate the redundancy
CalculScoresCalcul Score of a Sequence, using a loggods matrix
CalculSimilaritySimilarity Score between a Sequence and a PSSM model
chooseModelChooseModel: Choose the best model
classMODELclassMODEL: To choose the model
ConstructModelA set of functions for training of motif discovery...
correctionaproxCorrection Entropy Approximate from the Finite Sample Size...
correction.entropyCorrection entropy from the Finite Sample Size Effect
correction.redundancyCorrection redundancy from the Finite Sample Size Effect
CreateConsensusConsensus Sequence for a DNA motif
detectionDetection: A set of functions for detection of TFBS
detector_1rOrdre_diffDetection of Transcription Factor Binding Sites Through...
detector_2nOrdreDetection of Transcription Factor Binding Sites Through...
detector_2nOrdre_initDetection of Transcription Factor Binding Sites Through...
diffInstructionsThe measurement of the variation of the total redundancy
DivergenceDROSOPHILADivergenceDROSOPHILA: Given a Transcription factor chooses...
DivergenceHOMODivergenceHOMO: Given a Transcription factor chooses the...
DivergenceMUSDivergenceMUS: Given a Transcription factor chooses the model...
DivergenceRATTUSDivergenceRATTUS: Given a Transcription factor chooses the...
divergence.RenyiRenyi divergence
divergence.ShannonDivergencia.Shannon: Mutual Information
DrosophilaDivergenceA library of models for Divergence algorithm and _Drosophila...
DrosophilaEntropyA library of models for Entropy algorithm and _Drosophila...
DrosophilaQresidualsA library of models for Qresiduals algorithm and _Drosophila...
entropy.correctedCorrection of the Finite Sample Size Effect
EntropyDROSOPHILAEntropyDROSOPHILA: Given a Transcription factor chooses the...
EntropyHOMOEntropyHOMO: Given a Transcription factor chooses the model...
entropy.jointTo calculate joint entropy
EntropyMUSEntropyMUS: Given a Transcription factor chooses the model...
EntropyRATTUSEntropyRATTUS: Given a Transcription factor chooses the model...
entropy.RenyiRenyi Entropy
entropy.ShannonShannon Entropy
HmemoryLibrary of entropy values
HomoDivergenceA library of models for Divergence algorithm and _Homo...
HomoEntropyA library of models for Entropy algorithm and _Homo sapiens_...
HomoQresidualsA library of models for Qresiduals algorithm and _Homo...
HreadTo read Entropy values
iiccInitial conditions for the MEET package
JacksonParametersJacksonParameters: To calculates the parameters needed to...
joint.probabilityJoint Porbability
kfold.DivergenceLeave-one-out cross-training for parametric divergence...
kfold.EntropyLeave-one-out cross-training for Renyi entropy (ITEME)
kfold.MATCHMATCH training process
kfold.MDscanLeave-one-out cross-training for MDscan.
kfold.MEMELeave-one-out cross-training for MEME
kfold.PCAPCA
kfold.transMEMELeave-one-out cross-training for MEME/MAST through...
MEETMEET: Motif Elements Estimation Toolkit
MEET-packageMEET: Motif Elements Estimation Toolkit
MImemoryLibrary of PredictDivergence values
MIreadTo read PredictDivergence values
missing.funMissing values
ModelCreates a model class
ModelDivergenceTo create Model Divergence
ModelEntropyTo create Model Entropy
ModelMATCHMatch algorithm to detect TFBS in a sequence
ModelMDscanMDscan algortihm to detect TFBS within a sequence
ModelMEMEMEME algortihm to detect TFBS within a sequence
ModelPCAPCA model for a set of TFBS
ModelsTo create Detection Model
ModeltransMEMETo create Model transMEME
motif.mastRead output mast
MusDivergenceA library of models for Divergence algorithm and _Mus...
MusEntropyA library of models for Entropy algorithm and _Mus musculus_...
MusQresidualsA library of models for Qresiduals algorithm and _Mus...
numericalDNAConversion of nucleotides to numerical vectors
numericalTFMatrix of a numerical motif
organismMatrix of background frequencies
PCanalysisPC analysis on numerical DNA sequences
PredictDivergenceA set of functions for detection of Transcription Factor...
PredictEntropyPredictEntropy: Detection of Transcription Factor Binding...
PredictionTo detect Transcription Factor Binding sites by means of a...
PredictMATCHMATCH algorithm to detect TFBS in a sequence
PredictMDscanMDscan algorithm to detect TFBS in a sequence
PredictMEMEMEME algorithm to detect TFBS in a sequence
PredictPCAQ-residuals detection of TFBS, using a principal components...
PredicttransMEMEMAST algorithm to detect TFBS in a sequence
probabilityProbability
probability.coupleBackground joint probability
pvalueP value
QresidualsDROSOPHILAQresidualsDROSOPHILA: Given a Transcription factor chooses...
QresidualsHOMOQresidualsHOMO: Given a Transcription factor chooses the...
QresidualsMUSQresidualsMUS: Given a Transcription factor chooses the model...
QresidualsRATTUSQresidualsRATTUS: Given a Transcription factor chooses the...
QtoJacksonQ to Jackson: transform a Q-residual into a confidence...
RattusDivergenceA library of models for Divergence algorithm and _Rattus...
RattusEntropyA library of models for Entropy algorithm and _Rattus...
RattusQresidualsA library of models for Qresiduals algorithm and _Rattus...
Read.alignedRead nucleotide sequences
read.mastRead output mast
readMEMERead MEME motifs and consensus sequences
redundancyTo calculate redundancy
RenyiOrderRenyi entropy and Divergence order
ROCmodelTo choose the best paramater for a model
run.read.MDscanRun and read MDscan on training
scoreMDscanOutput MDscan method
SequenceSequence of a DNA motif
standardoutStandard output detector
TFlogoddsLogodds for a motif PSSM
TranscriptionFactorTranscription Factor Sequences
writeMEMEWrite a training matrix in a MEME/MAST format
writeResultsHTMLWrites the results of a MEET detection to HTML.
MEET documentation built on May 31, 2017, 4:10 a.m.