MEET: Motif Elements Estimation Toolkit

align.clustalw | Multiple sequence alignment by means of ClustalW |

align.MEME | Multiple sequence alignment by means of MEME. |

Alignment | To line up Transcription Factor Binding Sites through... |

align.muscle | Multiple sequence alignment by means of Muscle (MUltiple... |

BackgroundOrganism | Matrix of background frequencies |

CalculInformation | Information content in each position of a set of aligned DNA... |

CalculPSSM | Position Specific Scoring Matrices from a set of aligned... |

CalculPWM | CalculPWM: To calculate Position Weight Matrix |

CalculRedundancy | CalculRedundancy: To calculate the redundancy |

CalculScores | Calcul Score of a Sequence, using a loggods matrix |

CalculSimilarity | Similarity Score between a Sequence and a PSSM model |

chooseModel | ChooseModel: Choose the best model |

classMODEL | classMODEL: To choose the model |

ConstructModel | A set of functions for training of motif discovery... |

correctionaprox | Correction Entropy Approximate from the Finite Sample Size... |

correction.entropy | Correction entropy from the Finite Sample Size Effect |

correction.redundancy | Correction redundancy from the Finite Sample Size Effect |

CreateConsensus | Consensus Sequence for a DNA motif |

detection | Detection: A set of functions for detection of TFBS |

detector_1rOrdre_diff | Detection of Transcription Factor Binding Sites Through... |

detector_2nOrdre | Detection of Transcription Factor Binding Sites Through... |

detector_2nOrdre_init | Detection of Transcription Factor Binding Sites Through... |

diffInstructions | The measurement of the variation of the total redundancy |

DivergenceDROSOPHILA | DivergenceDROSOPHILA: Given a Transcription factor chooses... |

DivergenceHOMO | DivergenceHOMO: Given a Transcription factor chooses the... |

DivergenceMUS | DivergenceMUS: Given a Transcription factor chooses the model... |

DivergenceRATTUS | DivergenceRATTUS: Given a Transcription factor chooses the... |

divergence.Renyi | Renyi divergence |

divergence.Shannon | Divergencia.Shannon: Mutual Information |

DrosophilaDivergence | A library of models for Divergence algorithm and _Drosophila... |

DrosophilaEntropy | A library of models for Entropy algorithm and _Drosophila... |

DrosophilaQresiduals | A library of models for Qresiduals algorithm and _Drosophila... |

entropy.corrected | Correction of the Finite Sample Size Effect |

EntropyDROSOPHILA | EntropyDROSOPHILA: Given a Transcription factor chooses the... |

EntropyHOMO | EntropyHOMO: Given a Transcription factor chooses the model... |

entropy.joint | To calculate joint entropy |

EntropyMUS | EntropyMUS: Given a Transcription factor chooses the model... |

EntropyRATTUS | EntropyRATTUS: Given a Transcription factor chooses the model... |

entropy.Renyi | Renyi Entropy |

entropy.Shannon | Shannon Entropy |

Hmemory | Library of entropy values |

HomoDivergence | A library of models for Divergence algorithm and _Homo... |

HomoEntropy | A library of models for Entropy algorithm and _Homo sapiens_... |

HomoQresiduals | A library of models for Qresiduals algorithm and _Homo... |

Hread | To read Entropy values |

iicc | Initial conditions for the MEET package |

JacksonParameters | JacksonParameters: To calculates the parameters needed to... |

joint.probability | Joint Porbability |

kfold.Divergence | Leave-one-out cross-training for parametric divergence... |

kfold.Entropy | Leave-one-out cross-training for Renyi entropy (ITEME) |

kfold.MATCH | MATCH training process |

kfold.MDscan | Leave-one-out cross-training for MDscan. |

kfold.MEME | Leave-one-out cross-training for MEME |

kfold.PCA | PCA |

kfold.transMEME | Leave-one-out cross-training for MEME/MAST through... |

MEET | MEET: Motif Elements Estimation Toolkit |

MEET-package | MEET: Motif Elements Estimation Toolkit |

MImemory | Library of PredictDivergence values |

MIread | To read PredictDivergence values |

missing.fun | Missing values |

Model | Creates a model class |

ModelDivergence | To create Model Divergence |

ModelEntropy | To create Model Entropy |

ModelMATCH | Match algorithm to detect TFBS in a sequence |

ModelMDscan | MDscan algortihm to detect TFBS within a sequence |

ModelMEME | MEME algortihm to detect TFBS within a sequence |

ModelPCA | PCA model for a set of TFBS |

Models | To create Detection Model |

ModeltransMEME | To create Model transMEME |

motif.mast | Read output mast |

MusDivergence | A library of models for Divergence algorithm and _Mus... |

MusEntropy | A library of models for Entropy algorithm and _Mus musculus_... |

MusQresiduals | A library of models for Qresiduals algorithm and _Mus... |

numericalDNA | Conversion of nucleotides to numerical vectors |

numericalTF | Matrix of a numerical motif |

organism | Matrix of background frequencies |

PCanalysis | PC analysis on numerical DNA sequences |

PredictDivergence | A set of functions for detection of Transcription Factor... |

PredictEntropy | PredictEntropy: Detection of Transcription Factor Binding... |

Prediction | To detect Transcription Factor Binding sites by means of a... |

PredictMATCH | MATCH algorithm to detect TFBS in a sequence |

PredictMDscan | MDscan algorithm to detect TFBS in a sequence |

PredictMEME | MEME algorithm to detect TFBS in a sequence |

PredictPCA | Q-residuals detection of TFBS, using a principal components... |

PredicttransMEME | MAST algorithm to detect TFBS in a sequence |

probability | Probability |

probability.couple | Background joint probability |

pvalue | P value |

QresidualsDROSOPHILA | QresidualsDROSOPHILA: Given a Transcription factor chooses... |

QresidualsHOMO | QresidualsHOMO: Given a Transcription factor chooses the... |

QresidualsMUS | QresidualsMUS: Given a Transcription factor chooses the model... |

QresidualsRATTUS | QresidualsRATTUS: Given a Transcription factor chooses the... |

QtoJackson | Q to Jackson: transform a Q-residual into a confidence... |

RattusDivergence | A library of models for Divergence algorithm and _Rattus... |

RattusEntropy | A library of models for Entropy algorithm and _Rattus... |

RattusQresiduals | A library of models for Qresiduals algorithm and _Rattus... |

Read.aligned | Read nucleotide sequences |

read.mast | Read output mast |

readMEME | Read MEME motifs and consensus sequences |

redundancy | To calculate redundancy |

RenyiOrder | Renyi entropy and Divergence order |

ROCmodel | To choose the best paramater for a model |

run.read.MDscan | Run and read MDscan on training |

scoreMDscan | Output MDscan method |

Sequence | Sequence of a DNA motif |

standardout | Standard output detector |

TFlogodds | Logodds for a motif PSSM |

TranscriptionFactor | Transcription Factor Sequences |

writeMEME | Write a training matrix in a MEME/MAST format |

writeResultsHTML | Writes the results of a MEET detection to HTML. |

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