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).

Install the latest version of this package by entering the following in R:
install.packages("MEET")
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.

Functions

align.clustalw Man page
align.MEME Man page
Alignment Man page
align.muscle Man page
BackgroundOrganism Man page
CalculInformation Man page
CalculPSSM Man page
CalculPWM Man page
CalculRedundancy Man page
CalculScores Man page
CalculSimilarity Man page
chooseModel Man page
classMODEL Man page
ConstructModel Man page
correctionaprox Man page
correction-class Man page
correction.entropy Man page
correction.redundancy Man page
CreateConsensus Man page
detection Man page
detector_1rOrdre_diff Man page
detector_2nOrdre Man page
detector_2nOrdre_init Man page
diffInstructions Man page
DivergenceDROSOPHILA Man page
DivergenceHOMO Man page
DivergenceMUS Man page
DivergenceRATTUS Man page
divergence.Renyi Man page
divergence.Shannon Man page
entropy.corrected Man page
EntropyDROSOPHILA Man page
EntropyHOMO Man page
entropy.joint Man page
EntropyMUS Man page
EntropyRATTUS Man page
entropy.Renyi Man page
entropy.Shannon Man page
Hmemory Man page
Hread Man page
iicc Man page
JacksonParameters Man page
joint.probability Man page
kfold.Divergence Man page
kfold.Entropy Man page
kfold.MATCH Man page
kfold.MDscan Man page
kfold.MEME Man page
kfold.PCA Man page
kfold.transMEME Man page
MEET Man page
MImemory Man page
MIread Man page
Model-class Man page
ModelDivergence Man page
ModelEntropy Man page
ModelMATCH Man page
ModelMDscan Man page
ModelMEME Man page
ModelPCA Man page
Models Man page
ModeltransMEME Man page
motif.mast Man page
numericalDNA Man page
organism Man page
PCanalysis Man page
PredictDivergence Man page
PredictEntropy Man page
Prediction Man page
PredictMATCH Man page
PredictMDscan Man page
PredictMEME Man page
PredictPCA Man page
PredicttransMEME Man page
Prob Man page
probability Man page
probability.couple Man page
pvalue Man page
q Man page
QresidualsDROSOPHILA Man page
QresidualsHOMO Man page
QresidualsMUS Man page
QresidualsRATTUS Man page
QtoJackson Man page
Read.aligned Man page
read.mast Man page
readMEME Man page
ReadSequence Man page
redundancy Man page
ROCmodel Man page
run.read.MDscan Man page
scoreMDscan Man page
Sequence Man page
standardout Man page
TFlogodds Man page
TranscriptionFactor Man page
writeMEME Man page
writeResultsHTML Man page

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

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