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
ConstructModel          A set of functions for training of motif
                        discovery algorithms.
CreateConsensus         Consensus Sequence for a DNA motif
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.
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
JacksonParameters       JacksonParameters: To calculates the parameters
                        needed to transform a Q-residual to a
                        confidence interval
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
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
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
Prediction              To detect Transcription Factor Binding sites by
                        means of a 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.
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
ROCmodel                To choose the best paramater for a model
Read.aligned            Read nucleotide sequences
ReadSequence            Convert a DNA sequence in a numerical DNA
                        matrix
Sequence                A sequence with binding evidence.
TFlogodds               Logodds matrix
TranscriptionFactor     A set of aligned binding sites sequences
align.MEME              Multiple sequence alignment by means of MEME.
align.clustalw          Multiple sequence alignment by means of
                        ClustalW
align.muscle            Multiple sequence alignment by means of Muscle
                        (MUltiple Sequence Comparison by
                        Log-Expectation)
chooseModel             ChooseModel: Choose the best model
classMODEL              classMODEL: To choose the model
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.
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
entropy.Renyi           Renyi Entropy
entropy.Shannon         Shannon Entropy
entropy.corrected       Correction of the Finite Sample Size Effect
entropy.joint           To calculate joint entropy
iicc                    A set of initial conditions
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.
motif.mast              MEME format to training matrix
numericalDNA            Conversion of nucleotides to numerical vectors
organism                Probability for each nucleotide according to
                        different organism
probability             Probability
probability.couple      Background joint probability
pvalue                  P value
q                       Renyi Order
read.mast               Read output mast
readMEME                Read MEME motifs and consensus sequences
redundancy              To calculate redundancy
run.read.MDscan         Run and read MDscan on validation
scoreMDscan             Output MDscan method
standardout             Standard output detector
writeMEME               Write a training matrix in a MEME/MAST format
writeResultsHTML        Writes the results of a MEET detection to HTML.
