MEET: MEET: Motif Elements Estimation Toolkit
Version 5.1.1

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MEET")

Popular man pages

correction.entropy: Correction entropy from the Finite Sample Size Effect
entropy.joint: To calculate joint entropy
kfold.PCA: PCA
kfold.transMEME: Leave-one-out cross-validation for MEME/MAST through...
ModelPCA: PCA model for a set of TFBS
pvalue: P value
Sequence: A sequence with binding evidence.
See all...

All man pages Function index File listing

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.

Functions

Files

MD5
src
src/readH.c
src/probabilitycouple.c
src/probability.c
src/powX2.c
src/powRenyi.c
src/PCAdetection.c
src/modelgetList.h
src/missingfun.c
src/MI.c
src/loopENTROPY.c
src/loopDIVERGENCE.c
src/jointprobability.c
src/getListElement.c
src/entropyShannon.c
src/entropyRenyi.c
src/entropycorrected.c
src/divergenceShannon.c
src/correctionredundancy.c
src/correctionentropy.c
R
R/writeResultsHTML.R
R/writeMEME.R
R/standardout.R
R/scoreMDscan.R
R/run.read.MDscan.R
R/ROCmodel.R
R/redundancy.R
R/ReadSequence.R
R/readMEME.R
R/read.mast.R
R/Read.aligned.R
R/QtoJackson.R
R/QresidualsRATTUS.R
R/QresidualsMUS.R
R/QresidualsHOMO.R
R/QresidualsDROSOPHILA.R
R/pvalue.R
R/probability.R
R/probability.couple.R
R/PredicttransMEME.R
R/PredictPCA.R
R/PredictMEME.R
R/PredictMDscan.R
R/PredictMATCH.R
R/Prediction.R
R/PredictEntropy.R
R/PredictDivergence.R
R/PCanalysis.R
R/numericalDNA.R
R/motif.mast.R
R/ModeltransMEME.R
R/Models.R
R/ModelPCA.R
R/ModelMEME.R
R/ModelMDscan.R
R/ModelMATCH.R
R/ModelEntropy.R
R/ModelDivergence.R
R/Model.R
R/MIread.R
R/MImemory.R
R/MEET.R
R/kfold.transMEME.R
R/kfold.PCA.R
R/kfold.MEME.R
R/kfold.MDscan.R
R/kfold.MATCH.R
R/kfold.Entropy.R
R/kfold.Divergence.R
R/joint.probability.R
R/JacksonParameters.R
R/Hread.R
R/Hmemory.R
R/EntropyRATTUS.R
R/EntropyMUS.R
R/EntropyHOMO.R
R/EntropyDROSOPHILA.R
R/entropy.Shannon.R
R/entropy.Renyi.R
R/entropy.joint.R
R/entropy.corrected.R
R/DivergenceRATTUS.R
R/DivergenceMUS.R
R/DivergenceHOMO.R
R/DivergenceDROSOPHILA.R
R/divergence.Shannon.R
R/divergence.Renyi.R
R/diffInstructions.R
R/detector_2nOrdre_init.R
R/detector_2nOrdre.R
R/detector_1rOrdre_diff.R
R/detection.R
R/CreateConsensus.R
R/correctionaprox.R
R/correction.redundancy.R
R/correction.R
R/correction.entropy.R
R/ConstructModel.R
R/classMODEL.R
R/chooseModel.R
R/CalculSimilarity.R
R/CalculScores.R
R/CalculRedundancy.R
R/CalculPWM.R
R/CalculPSSM.R
R/CalculInformation.R
R/Alignment.R
R/align.muscle.R
R/align.MEME.R
R/align.clustalw.R
NAMESPACE
man
man/writeResultsHTML.Rd
man/writeMEME.Rd
man/TranscriptionFactor.Rd
man/TFlogodds.Rd
man/standardout.Rd
man/Sequence.Rd
man/scoreMDscan.Rd
man/run.read.MDscan.Rd
man/ROCmodel.Rd
man/redundancy.Rd
man/ReadSequence.Rd
man/readMEME.Rd
man/read.mast.Rd
man/Read.aligned.Rd
man/QtoJackson.Rd
man/QresidualsRATTUS.Rd
man/QresidualsMUS.Rd
man/QresidualsHOMO.Rd
man/QresidualsDROSOPHILA.Rd
man/q.Rd
man/pvalue.Rd
man/probability.Rd
man/probability.couple.Rd
man/Prob.Rd
man/PredicttransMEME.Rd
man/PredictPCA.Rd
man/PredictMEME.Rd
man/PredictMDscan.Rd
man/PredictMATCH.Rd
man/Prediction.Rd
man/PredictEntropy.Rd
man/PredictDivergence.Rd
man/PCanalysis.Rd
man/organism.Rd
man/numericalDNA.Rd
man/motif.mast.Rd
man/ModeltransMEME.Rd
man/Models.Rd
man/ModelPCA.Rd
man/ModelMEME.Rd
man/ModelMDscan.Rd
man/ModelMATCH.Rd
man/ModelEntropy.Rd
man/ModelDivergence.Rd
man/Model.Rd
man/MIread.Rd
man/MImemory.Rd
man/MEET.Rd
man/kfold.transMEME.Rd
man/kfold.PCA.Rd
man/kfold.MEME.Rd
man/kfold.MDscan.Rd
man/kfold.MATCH.Rd
man/kfold.Entropy.Rd
man/kfold.Divergence.Rd
man/joint.probability.Rd
man/JacksonParameters.Rd
man/iicc.Rd
man/Hread.Rd
man/Hmemory.Rd
man/EntropyRATTUS.Rd
man/EntropyMUS.Rd
man/EntropyHOMO.Rd
man/EntropyDROSOPHILA.Rd
man/entropy.Shannon.Rd
man/entropy.Renyi.Rd
man/entropy.joint.Rd
man/entropy.corrected.Rd
man/DivergenceRATTUS.Rd
man/DivergenceMUS.Rd
man/DivergenceHOMO.Rd
man/DivergenceDROSOPHILA.Rd
man/divergence.Shannon.Rd
man/divergence.Renyi.Rd
man/diffInstructions.Rd
man/detector_2nOrdre_init.Rd
man/detector_2nOrdre.Rd
man/detector_1rOrdre_diff.Rd
man/detection.Rd
man/CreateConsensus.Rd
man/correctionaprox.Rd
man/correction.redundancy.Rd
man/correction.Rd
man/correction.entropy.Rd
man/ConstructModel.Rd
man/classMODEL.Rd
man/chooseModel.Rd
man/CalculSimilarity.Rd
man/CalculScores.Rd
man/CalculRedundancy.Rd
man/CalculPWM.Rd
man/CalculPSSM.Rd
man/CalculInformation.Rd
man/BackgroundOrganism.Rd
man/Alignment.Rd
man/align.muscle.Rd
man/align.MEME.Rd
man/align.clustalw.Rd
inst
inst/sequences
inst/sequences/FOXO301.fasta
inst/sequences/DNAtostudy.fa
inst/sequences/DNAmeet.afa
inst/sequences/DNAhomo.fa
inst/sequences/AP1.fa
exec
exec/webmeet.js
exec/webmeet.csa.css
exec/LogoMEET.png
exec/jquery.js
exec/jquery.cluetip.js
exec/jquery.cluetip.csa.css
exec/jquery-ui-1.8.20.custom.min.js
exec/jquery-ui-1.8.20.custom.csa.css
DESCRIPTION
data
data/TranscriptionFactor.rda
data/TFlogodds.rda
data/Sequence.rda
data/RenyiOrder.rda
data/RattusQresiduals.rda
data/RattusEntropy.rda
data/RattusDivergence.rda
data/organism.rda
data/MusQresiduals.rda
data/MusEntropy.rda
data/MusDivergence.rda
data/iicc.rda
data/HomoQresiduals.rda
data/HomoEntropy.rda
data/HomoDivergence.rda
data/DrosophilaQresiduals.rda
data/DrosophilaEntropy.rda
data/DrosophilaDivergence.rda
data/datalist
data/BackgroundOrganism.rda
MEET documentation built on May 20, 2017, 2:32 a.m.

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