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...
BackgroundOrganismProbabilities of each nucleotide in the _Homo sapiens_...
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...
correctionCorrection for finite sample effect
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
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
HreadTo read Entropy values
iiccA set of initial conditions
JacksonParametersJacksonParameters: To calculates the parameters needed to...
joint.probabilityJoint Probability
kfold.DivergenceLeave-one-out cross-validation for parametric divergence...
kfold.EntropyLeave-one-out cross-validation for Renyi entropy (ITEME)
kfold.MATCHMATCH validation process
kfold.MDscanLeave-one-out cross-validation for MDscan.
kfold.MEMELeave-one-out cross-validation for MEME
kfold.PCAPCA
kfold.transMEMELeave-one-out cross-validation for MEME/MAST through...
MEETMEET: Motif Elements Estimation Toolkit
MImemoryLibrary of PredictDivergence values
MIreadTo read PredictDivergence values
ModelA set of Models for the detection
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.mastMEME format to training matrix
numericalDNAConversion of nucleotides to numerical vectors
organismProbability for each nucleotide according to different...
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
ProbProbabilities of each nucleotide in the _Homo sapiens_...
probabilityProbability
probability.coupleBackground joint probability
pvalueP value
qRenyi Order
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...
Read.alignedRead nucleotide sequences
read.mastRead output mast
readMEMERead MEME motifs and consensus sequences
ReadSequenceConvert a DNA sequence in a numerical DNA matrix
redundancyTo calculate redundancy
ROCmodelTo choose the best paramater for a model
run.read.MDscanRun and read MDscan on validation
scoreMDscanOutput MDscan method
SequenceA sequence with binding evidence.
standardoutStandard output detector
TFlogoddsLogodds matrix
TranscriptionFactorA set of aligned binding sites sequences
writeMEMEWrite a training matrix in a MEME/MAST format
writeResultsHTMLWrites the results of a MEET detection to HTML.
MEET documentation built on May 30, 2017, 4:56 a.m.