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| align.clustalw | Multiple sequence alignment by means of ClustalW |
| align.MEME | Multiple sequence alignment by means of MEME. |
| align.muscle | Multiple sequence alignment by means of Muscle (MUltiple Sequence Comparison by Log-Expectation) |
| Alignment | To line up Transcription Factor Binding sites through Multiple Sequence Alignment (MSA) |
| BackgroundOrganism | Probabilities of each nucleotide in the _Homo sapiens_ organism according to Thakurta et al. |
| CalculInformation | Information content in each position of a set of aligned DNA sequences |
| CalculPSSM | Position Specific Scoring Matrices from a set of aligned sequences |
| 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 algorithms. |
| correction-class | Correction for finite sample effect |
| correction.entropy | Correction entropy from the Finite Sample Size Effect |
| correction.redundancy | Correction redundancy from the Finite Sample Size Effect |
| correctionaprox | Correction Entropy Approximate 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 Differential Renyi Entropy |
| detector_2nOrdre | Detection of Transcription Factor Binding Sites Through Parametric PredictDivergence |
| detector_2nOrdre_init | Detection of Transcription Factor Binding Sites Through Parametric PredictDivergence |
| diffInstructions | The measurement of the variation of the total redundancy |
| divergence.Renyi | Renyi divergence |
| divergence.Shannon | Divergencia.Shannon: Mutual Information |
| DivergenceDROSOPHILA | DivergenceDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method. |
| DivergenceHOMO | DivergenceHOMO: Given a Transcription factor chooses the model for a specific organism and method. |
| DivergenceMUS | DivergenceMUS: Given a Transcription factor chooses the model for a specific organism and method. |
| DivergenceRATTUS | DivergenceRATTUS: Given a Transcription factor chooses the model for a specific organism and method. |
| entropy.corrected | Correction of the Finite Sample Size Effect |
| entropy.joint | To calculate joint entropy |
| entropy.Renyi | Renyi Entropy |
| entropy.Shannon | Shannon Entropy |
| EntropyDROSOPHILA | EntropyDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method. |
| EntropyHOMO | EntropyHOMO: Given a Transcription factor chooses the model for a specific organism and method. |
| EntropyMUS | EntropyMUS: Given a Transcription factor chooses the model for a specific organism and method. |
| EntropyRATTUS | EntropyRATTUS: Given a Transcription factor chooses the model for a specific organism and method. |
| Hmemory | Library of entropy values |
| Hread | To read Entropy values |
| iicc | A set of initial conditions |
| JacksonParameters | JacksonParameters: To calculates the parameters needed to transform a Q-residual to a confidence interval |
| joint.probability | Joint Probability |
| kfold.Divergence | Leave-one-out cross-validation for parametric divergence (ITEME). |
| kfold.Entropy | Leave-one-out cross-validation for Renyi entropy (ITEME) |
| kfold.MATCH | MATCH validation process |
| kfold.MDscan | Leave-one-out cross-validation for MDscan. |
| kfold.MEME | Leave-one-out cross-validation for MEME |
| kfold.PCA | PCA |
| kfold.transMEME | Leave-one-out cross-validation for MEME/MAST through training.matrix aligned with MUSCLE or CLUSTALW. |
| MEET | MEET: Motif Elements Estimation Toolkit |
| MImemory | Library of PredictDivergence values |
| MIread | To read PredictDivergence values |
| Model-class | A set of Models for the detection |
| 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 | MEME format to training matrix |
| numericalDNA | Conversion of nucleotides to numerical vectors |
| organism | Probability for each nucleotide according to different organism |
| PCanalysis | PC analysis on numerical DNA sequences |
| PredictDivergence | A set of functions for detection of Transcription Factor Binding Sites by means of Divergence |
| PredictEntropy | PredictEntropy: Detection of Transcription Factor Binding Sites by means of Renyi entropy |
| Prediction | To detect Transcription Factor Binding sites by means of a model |
| 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 model |
| PredicttransMEME | MAST algorithm to detect TFBS in a sequence |
| Prob | Probabilities of each nucleotide in the _Homo sapiens_ organism according to Thakurta et al. |
| probability | Probability |
| probability.couple | Background joint probability |
| pvalue | P value |
| q | Renyi Order |
| QresidualsDROSOPHILA | QresidualsDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method. |
| QresidualsHOMO | QresidualsHOMO: Given a Transcription factor chooses the model for a specific organism and method. |
| QresidualsMUS | QresidualsMUS: Given a Transcription factor chooses the model for a specific organism and method. |
| QresidualsRATTUS | QresidualsRATTUS: Given a Transcription factor chooses the model for a specific organism and method. |
| QtoJackson | Q to Jackson: transform a Q-residual into a confidence interval |
| Read.aligned | Read nucleotide sequences |
| read.mast | Read output mast |
| readMEME | Read MEME motifs and consensus sequences |
| ReadSequence | Convert a DNA sequence in a numerical DNA matrix |
| redundancy | To calculate redundancy |
| ROCmodel | To choose the best paramater for a model |
| run.read.MDscan | Run and read MDscan on validation |
| scoreMDscan | Output MDscan method |
| Sequence | A sequence with binding evidence. |
| standardout | Standard output detector |
| TFlogodds | Logodds matrix |
| TranscriptionFactor | A set of aligned binding sites sequences |
| writeMEME | Write a training matrix in a MEME/MAST format |
| writeResultsHTML | Writes the results of a MEET detection to HTML. |