MEET: MEET: Motif Elements Estimation Toolkit

MEET (Motif Elements Estimation Toolkit) is a R-package that integrates a set of computational algorithms for the detection of Transcription Factor Binding Sites (TFBS).

AuthorJoan Maynou and Erola Pairo.
Date of publication2013-02-22 16:07:16
MaintainerJoan Maynou <joan.maynou@upc.edu>
LicenseGPL (>= 2)
Version5.1.1

View on CRAN

Man pages

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: Probabilities of each nucleotide in the _Homo sapiens_...

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...

correction: Correction for finite sample effect

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

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

Hread: To read Entropy values

iicc: A set of initial conditions

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

joint.probability: Joint Probability

kfold.Divergence: Leave-one-out cross-validation for parametric divergence...

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...

MEET: MEET: Motif Elements Estimation Toolkit

MImemory: Library of PredictDivergence values

MIread: To read PredictDivergence values

Model: 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...

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

Prob: Probabilities of each nucleotide in the _Homo sapiens_...

probability: Probability

probability.couple: Background joint probability

pvalue: P value

q: Renyi Order

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...

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.

Files in this package

MEET
MEET/MD5
MEET/src
MEET/src/readH.c
MEET/src/probabilitycouple.c
MEET/src/probability.c
MEET/src/powX2.c
MEET/src/powRenyi.c
MEET/src/PCAdetection.c
MEET/src/modelgetList.h
MEET/src/missingfun.c
MEET/src/MI.c
MEET/src/loopENTROPY.c
MEET/src/loopDIVERGENCE.c
MEET/src/jointprobability.c
MEET/src/getListElement.c
MEET/src/entropyShannon.c
MEET/src/entropyRenyi.c
MEET/src/entropycorrected.c
MEET/src/divergenceShannon.c
MEET/src/correctionredundancy.c
MEET/src/correctionentropy.c
MEET/R
MEET/R/writeResultsHTML.R MEET/R/writeMEME.R MEET/R/standardout.R MEET/R/scoreMDscan.R MEET/R/run.read.MDscan.R MEET/R/ROCmodel.R MEET/R/redundancy.R MEET/R/ReadSequence.R MEET/R/readMEME.R MEET/R/read.mast.R MEET/R/Read.aligned.R MEET/R/QtoJackson.R MEET/R/QresidualsRATTUS.R MEET/R/QresidualsMUS.R MEET/R/QresidualsHOMO.R MEET/R/QresidualsDROSOPHILA.R MEET/R/pvalue.R MEET/R/probability.R MEET/R/probability.couple.R MEET/R/PredicttransMEME.R MEET/R/PredictPCA.R MEET/R/PredictMEME.R MEET/R/PredictMDscan.R MEET/R/PredictMATCH.R MEET/R/Prediction.R MEET/R/PredictEntropy.R MEET/R/PredictDivergence.R MEET/R/PCanalysis.R MEET/R/numericalDNA.R MEET/R/motif.mast.R MEET/R/ModeltransMEME.R MEET/R/Models.R MEET/R/ModelPCA.R MEET/R/ModelMEME.R MEET/R/ModelMDscan.R MEET/R/ModelMATCH.R MEET/R/ModelEntropy.R MEET/R/ModelDivergence.R MEET/R/Model.R MEET/R/MIread.R MEET/R/MImemory.R MEET/R/MEET.R MEET/R/kfold.transMEME.R MEET/R/kfold.PCA.R MEET/R/kfold.MEME.R MEET/R/kfold.MDscan.R MEET/R/kfold.MATCH.R MEET/R/kfold.Entropy.R MEET/R/kfold.Divergence.R MEET/R/joint.probability.R MEET/R/JacksonParameters.R MEET/R/Hread.R MEET/R/Hmemory.R MEET/R/EntropyRATTUS.R MEET/R/EntropyMUS.R MEET/R/EntropyHOMO.R MEET/R/EntropyDROSOPHILA.R MEET/R/entropy.Shannon.R MEET/R/entropy.Renyi.R MEET/R/entropy.joint.R MEET/R/entropy.corrected.R MEET/R/DivergenceRATTUS.R MEET/R/DivergenceMUS.R MEET/R/DivergenceHOMO.R MEET/R/DivergenceDROSOPHILA.R MEET/R/divergence.Shannon.R MEET/R/divergence.Renyi.R MEET/R/diffInstructions.R MEET/R/detector_2nOrdre_init.R MEET/R/detector_2nOrdre.R MEET/R/detector_1rOrdre_diff.R MEET/R/detection.R MEET/R/CreateConsensus.R MEET/R/correctionaprox.R MEET/R/correction.redundancy.R MEET/R/correction.R MEET/R/correction.entropy.R MEET/R/ConstructModel.R MEET/R/classMODEL.R MEET/R/chooseModel.R MEET/R/CalculSimilarity.R MEET/R/CalculScores.R MEET/R/CalculRedundancy.R MEET/R/CalculPWM.R MEET/R/CalculPSSM.R MEET/R/CalculInformation.R MEET/R/Alignment.R MEET/R/align.muscle.R MEET/R/align.MEME.R MEET/R/align.clustalw.R
MEET/NAMESPACE
MEET/man
MEET/man/writeResultsHTML.Rd MEET/man/writeMEME.Rd MEET/man/TranscriptionFactor.Rd MEET/man/TFlogodds.Rd MEET/man/standardout.Rd MEET/man/Sequence.Rd MEET/man/scoreMDscan.Rd MEET/man/run.read.MDscan.Rd MEET/man/ROCmodel.Rd MEET/man/redundancy.Rd MEET/man/ReadSequence.Rd MEET/man/readMEME.Rd MEET/man/read.mast.Rd MEET/man/Read.aligned.Rd MEET/man/QtoJackson.Rd MEET/man/QresidualsRATTUS.Rd MEET/man/QresidualsMUS.Rd MEET/man/QresidualsHOMO.Rd MEET/man/QresidualsDROSOPHILA.Rd MEET/man/q.Rd MEET/man/pvalue.Rd MEET/man/probability.Rd MEET/man/probability.couple.Rd MEET/man/Prob.Rd MEET/man/PredicttransMEME.Rd MEET/man/PredictPCA.Rd MEET/man/PredictMEME.Rd MEET/man/PredictMDscan.Rd MEET/man/PredictMATCH.Rd MEET/man/Prediction.Rd MEET/man/PredictEntropy.Rd MEET/man/PredictDivergence.Rd MEET/man/PCanalysis.Rd MEET/man/organism.Rd MEET/man/numericalDNA.Rd MEET/man/motif.mast.Rd MEET/man/ModeltransMEME.Rd MEET/man/Models.Rd MEET/man/ModelPCA.Rd MEET/man/ModelMEME.Rd MEET/man/ModelMDscan.Rd MEET/man/ModelMATCH.Rd MEET/man/ModelEntropy.Rd MEET/man/ModelDivergence.Rd MEET/man/Model.Rd MEET/man/MIread.Rd MEET/man/MImemory.Rd MEET/man/MEET.Rd MEET/man/kfold.transMEME.Rd MEET/man/kfold.PCA.Rd MEET/man/kfold.MEME.Rd MEET/man/kfold.MDscan.Rd MEET/man/kfold.MATCH.Rd MEET/man/kfold.Entropy.Rd MEET/man/kfold.Divergence.Rd MEET/man/joint.probability.Rd MEET/man/JacksonParameters.Rd MEET/man/iicc.Rd MEET/man/Hread.Rd MEET/man/Hmemory.Rd MEET/man/EntropyRATTUS.Rd MEET/man/EntropyMUS.Rd MEET/man/EntropyHOMO.Rd MEET/man/EntropyDROSOPHILA.Rd MEET/man/entropy.Shannon.Rd MEET/man/entropy.Renyi.Rd MEET/man/entropy.joint.Rd MEET/man/entropy.corrected.Rd MEET/man/DivergenceRATTUS.Rd MEET/man/DivergenceMUS.Rd MEET/man/DivergenceHOMO.Rd MEET/man/DivergenceDROSOPHILA.Rd MEET/man/divergence.Shannon.Rd MEET/man/divergence.Renyi.Rd MEET/man/diffInstructions.Rd MEET/man/detector_2nOrdre_init.Rd MEET/man/detector_2nOrdre.Rd MEET/man/detector_1rOrdre_diff.Rd MEET/man/detection.Rd MEET/man/CreateConsensus.Rd MEET/man/correctionaprox.Rd MEET/man/correction.redundancy.Rd MEET/man/correction.Rd MEET/man/correction.entropy.Rd MEET/man/ConstructModel.Rd MEET/man/classMODEL.Rd MEET/man/chooseModel.Rd MEET/man/CalculSimilarity.Rd MEET/man/CalculScores.Rd MEET/man/CalculRedundancy.Rd MEET/man/CalculPWM.Rd MEET/man/CalculPSSM.Rd MEET/man/CalculInformation.Rd MEET/man/BackgroundOrganism.Rd MEET/man/Alignment.Rd MEET/man/align.muscle.Rd MEET/man/align.MEME.Rd MEET/man/align.clustalw.Rd
MEET/inst
MEET/inst/sequences
MEET/inst/sequences/FOXO301.fasta
MEET/inst/sequences/DNAtostudy.fa
MEET/inst/sequences/DNAmeet.afa
MEET/inst/sequences/DNAhomo.fa
MEET/inst/sequences/AP1.fa
MEET/exec
MEET/exec/webmeet.js
MEET/exec/webmeet.csa.css
MEET/exec/LogoMEET.png
MEET/exec/jquery.js
MEET/exec/jquery.cluetip.js
MEET/exec/jquery.cluetip.csa.css
MEET/exec/jquery-ui-1.8.20.custom.min.js
MEET/exec/jquery-ui-1.8.20.custom.csa.css
MEET/DESCRIPTION
MEET/data
MEET/data/TranscriptionFactor.rda
MEET/data/TFlogodds.rda
MEET/data/Sequence.rda
MEET/data/RenyiOrder.rda
MEET/data/RattusQresiduals.rda
MEET/data/RattusEntropy.rda
MEET/data/RattusDivergence.rda
MEET/data/organism.rda
MEET/data/MusQresiduals.rda
MEET/data/MusEntropy.rda
MEET/data/MusDivergence.rda
MEET/data/iicc.rda
MEET/data/HomoQresiduals.rda
MEET/data/HomoEntropy.rda
MEET/data/HomoDivergence.rda
MEET/data/DrosophilaQresiduals.rda
MEET/data/DrosophilaEntropy.rda
MEET/data/DrosophilaDivergence.rda
MEET/data/datalist
MEET/data/BackgroundOrganism.rda

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