MEET: MEET: Motif Elements Estimation Toolkit

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MEET is an R-package that includes a set of models and tools for the detection of cis-regulatory sequences.

Author
Erola Pairo and Joan Maynou.
Date of publication
None
Maintainer
Erola Pairo <epairo@ibecbarcelona.eu> and Joan Maynou <joan.maynou@upc.edu>
License
GPL(>=2)
Version
5.1

View on R-Forge

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
Matrix of background frequencies
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...
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
DrosophilaDivergence
A library of models for Divergence algorithm and _Drosophila...
DrosophilaEntropy
A library of models for Entropy algorithm and _Drosophila...
DrosophilaQresiduals
A library of models for Qresiduals algorithm and _Drosophila...
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
HomoDivergence
A library of models for Divergence algorithm and _Homo...
HomoEntropy
A library of models for Entropy algorithm and _Homo sapiens_...
HomoQresiduals
A library of models for Qresiduals algorithm and _Homo...
Hread
To read Entropy values
iicc
Initial conditions for the MEET package
JacksonParameters
JacksonParameters: To calculates the parameters needed to...
joint.probability
Joint Porbability
kfold.Divergence
Leave-one-out cross-training for parametric divergence...
kfold.Entropy
Leave-one-out cross-training for Renyi entropy (ITEME)
kfold.MATCH
MATCH training process
kfold.MDscan
Leave-one-out cross-training for MDscan.
kfold.MEME
Leave-one-out cross-training for MEME
kfold.PCA
PCA
kfold.transMEME
Leave-one-out cross-training for MEME/MAST through...
MEET
MEET: Motif Elements Estimation Toolkit
MEET-package
MEET: Motif Elements Estimation Toolkit
MImemory
Library of PredictDivergence values
MIread
To read PredictDivergence values
missing.fun
Missing values
Model
Creates a model class
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
Read output mast
MusDivergence
A library of models for Divergence algorithm and _Mus...
MusEntropy
A library of models for Entropy algorithm and _Mus musculus_...
MusQresiduals
A library of models for Qresiduals algorithm and _Mus...
numericalDNA
Conversion of nucleotides to numerical vectors
numericalTF
Matrix of a numerical motif
organism
Matrix of background frequencies
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
probability
Probability
probability.couple
Background joint probability
pvalue
P value
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...
RattusDivergence
A library of models for Divergence algorithm and _Rattus...
RattusEntropy
A library of models for Entropy algorithm and _Rattus...
RattusQresiduals
A library of models for Qresiduals algorithm and _Rattus...
Read.aligned
Read nucleotide sequences
read.mast
Read output mast
readMEME
Read MEME motifs and consensus sequences
redundancy
To calculate redundancy
RenyiOrder
Renyi entropy and Divergence order
ROCmodel
To choose the best paramater for a model
run.read.MDscan
Run and read MDscan on training
scoreMDscan
Output MDscan method
Sequence
Sequence of a DNA motif
standardout
Standard output detector
TFlogodds
Logodds for a motif PSSM
TranscriptionFactor
Transcription Factor 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/NAMESPACE
MEET/data
MEET/data/organism.rda
MEET/data/.Rapp.history
MEET/data/HomoEntropy.rda
MEET/data/DrosophilaEntropy.rda
MEET/data/RattusDivergence.rda
MEET/data/TFlogodds.rda
MEET/data/MusQresiduals.rda
MEET/data/RattusEntropy.rda
MEET/data/RenyiOrder.rda
MEET/data/iicc.rda
MEET/data/DrosophilaQresiduals.rda
MEET/data/HomoQresiduals.rda
MEET/data/datalist
MEET/data/DrosophilaDivergence.rda
MEET/data/numericalTF.rda
MEET/data/RattusQresiduals.rda
MEET/data/Sequence.rda
MEET/data/MusDivergence.rda
MEET/data/BackgroundOrganism.rda
MEET/data/MusEntropy.rda
MEET/data/HomoDivergence.rda
MEET/data/TranscriptionFactor.rda
MEET/R
MEET/R/Alignment.R
MEET/R/entropy.Shannon.R
MEET/R/ModeltransMEME.R
MEET/R/probability.couple.R
MEET/R/redundancy.R
MEET/R/EntropyDROSOPHILA.R
MEET/R/PredictMDscan.R
MEET/R/CalculScores.R
MEET/R/kfold.Divergence.R
MEET/R/standardout.R
MEET/R/diffInstructions.R
MEET/R/entropy.joint.R
MEET/R/joint.probability.R
MEET/R/detector_2nOrdre_init.R
MEET/R/run.read.MDscan.R
MEET/R/ModelPCA.R
MEET/R/read.mast.R
MEET/R/numericalDNA.R
MEET/R/kfold.Entropy.R
MEET/R/writeResultsHTML.R
MEET/R/chooseModel.R
MEET/R/CalculRedundancy.R
MEET/R/CalculInformation.R
MEET/R/CalculPSSM.R
MEET/R/entropy.corrected.R
MEET/R/ConstructModel.R
MEET/R/ModelMDscan.R
MEET/R/ModelDivergence.R
MEET/R/ModelMEME.R
MEET/R/ROCmodel.R
MEET/R/MImemory.R
MEET/R/divergence.Renyi.R
MEET/R/EntropyMUS.R
MEET/R/align.clustalw.R
MEET/R/EntropyHOMO.R
MEET/R/Models.R
MEET/R/kfold.MEME.R
MEET/R/Read.aligned.R
MEET/R/align.muscle.R
MEET/R/divergence.Shannon.R
MEET/R/kfold.MATCH.R
MEET/R/DivergenceRATTUS.R
MEET/R/PredicttransMEME.R
MEET/R/correctionaprox.R
MEET/R/Hmemory.R
MEET/R/PredictMEME.R
MEET/R/PredictPCA.R
MEET/R/CreateConsensus.R
MEET/R/MEET.R
MEET/R/DivergenceMUS.R
MEET/R/probability.R
MEET/R/scoreMDscan.R
MEET/R/align.MEME.R
MEET/R/QresidualsMUS.R
MEET/R/Hread.R
MEET/R/JacksonParameters.R
MEET/R/DivergenceDROSOPHILA.R
MEET/R/ModelEntropy.R
MEET/R/ModelMATCH.R
MEET/R/PredictDivergence.R
MEET/R/kfold.MDscan.R
MEET/R/kfold.transMEME.R
MEET/R/CalculPWM.R
MEET/R/kfold.PCA.R
MEET/R/QresidualsHOMO.R
MEET/R/QresidualsDROSOPHILA.R
MEET/R/writeMEME.R
MEET/R/QresidualsRATTUS.R
MEET/R/CalculSimilarity.R
MEET/R/QtoJackson.R
MEET/R/correction.entropy.R
MEET/R/PCanalysis.R
MEET/R/detector_2nOrdre.R
MEET/R/readMEME.R
MEET/R/PredictMATCH.R
MEET/R/pvalue.R
MEET/R/classMODEL.R
MEET/R/motif.mast.R
MEET/R/detection.R
MEET/R/correction.redundancy.R
MEET/R/correction.R
MEET/R/Prediction.R
MEET/R/detector_1rOrdre_diff.R
MEET/R/DivergenceHOMO.R
MEET/R/missing.fun.R
MEET/R/PredictEntropy.R
MEET/R/entropy.Renyi.R
MEET/R/Model.R
MEET/R/EntropyRATTUS.R
MEET/R/MIread.R
MEET/exec
MEET/exec/jquery-ui-1.8.20.custom.css
MEET/exec/jquery.cluetip.js
MEET/exec/jquery.js
MEET/exec/webmeet.js
MEET/exec/jquery.cluetip.css
MEET/exec/webmeet.css
MEET/exec/LogoMEET.png
MEET/exec/jquery-ui-1.8.20.custom.min.js
MEET/inst
MEET/inst/exdata
MEET/inst/exdata/AP1.fa
MEET/inst/exdata/DNAmeet.afa
MEET/inst/exdata/DNAhomo.fa
MEET/inst/exdata/DNAtostudy.fa
MEET/DESCRIPTION
MEET/man
MEET/man/DrosophilaDivergence.Rd
MEET/man/QresidualsDROSOPHILA.Rd
MEET/man/CalculPWM.Rd
MEET/man/Models.Rd
MEET/man/PredictMDscan.Rd
MEET/man/correction.redundancy.Rd
MEET/man/standardout.Rd
MEET/man/EntropyMUS.Rd
MEET/man/writeMEME.Rd
MEET/man/PCanalysis.Rd
MEET/man/redundancy.Rd
MEET/man/PredicttransMEME.Rd
MEET/man/probability.couple.Rd
MEET/man/kfold.MATCH.Rd
MEET/man/Model.Rd
MEET/man/detector_2nOrdre_init.Rd
MEET/man/CreateConsensus.Rd
MEET/man/DivergenceDROSOPHILA.Rd
MEET/man/TFlogodds.Rd
MEET/man/DivergenceRATTUS.Rd
MEET/man/kfold.MDscan.Rd
MEET/man/ModelMDscan.Rd
MEET/man/scoreMDscan.Rd
MEET/man/MEET.Rd
MEET/man/QresidualsHOMO.Rd
MEET/man/EntropyDROSOPHILA.Rd
MEET/man/ModelMEME.Rd
MEET/man/joint.probability.Rd
MEET/man/EntropyHOMO.Rd
MEET/man/MEET-package.Rd
MEET/man/readMEME.Rd
MEET/man/divergence.Renyi.Rd
MEET/man/PredictEntropy.Rd
MEET/man/align.clustalw.Rd
MEET/man/ModelPCA.Rd
MEET/man/correctionaprox.Rd
MEET/man/iicc.Rd
MEET/man/organism.Rd
MEET/man/JacksonParameters.Rd
MEET/man/CalculRedundancy.Rd
MEET/man/HomoQresiduals.Rd
MEET/man/Sequence.Rd
MEET/man/ConstructModel.Rd
MEET/man/detector_2nOrdre.Rd
MEET/man/Prediction.Rd
MEET/man/kfold.Entropy.Rd
MEET/man/TranscriptionFactor.Rd
MEET/man/DivergenceMUS.Rd
MEET/man/kfold.transMEME.Rd
MEET/man/HomoEntropy.Rd
MEET/man/MIread.Rd
MEET/man/HomoDivergence.Rd
MEET/man/EntropyRATTUS.Rd
MEET/man/run.read.MDscan.Rd
MEET/man/motif.mast.Rd
MEET/man/ModelEntropy.Rd
MEET/man/PredictMATCH.Rd
MEET/man/pvalue.Rd
MEET/man/entropy.Shannon.Rd
MEET/man/CalculScores.Rd
MEET/man/QresidualsMUS.Rd
MEET/man/DrosophilaEntropy.Rd
MEET/man/Hread.Rd
MEET/man/RenyiOrder.Rd
MEET/man/entropy.joint.Rd
MEET/man/BackgroundOrganism.Rd
MEET/man/DivergenceHOMO.Rd
MEET/man/CalculSimilarity.Rd
MEET/man/writeResultsHTML.Rd
MEET/man/MImemory.Rd
MEET/man/RattusDivergence.Rd
MEET/man/RattusQresiduals.Rd
MEET/man/chooseModel.Rd
MEET/man/QresidualsRATTUS.Rd
MEET/man/Alignment.Rd
MEET/man/PredictDivergence.Rd
MEET/man/numericalDNA.Rd
MEET/man/Read.aligned.Rd
MEET/man/align.muscle.Rd
MEET/man/MusEntropy.Rd
MEET/man/ModelMATCH.Rd
MEET/man/diffInstructions.Rd
MEET/man/read.mast.Rd
MEET/man/CalculInformation.Rd
MEET/man/entropy.Renyi.Rd
MEET/man/divergence.Shannon.Rd
MEET/man/PredictMEME.Rd
MEET/man/kfold.PCA.Rd
MEET/man/kfold.MEME.Rd
MEET/man/correction.entropy.Rd
MEET/man/DrosophilaQresiduals.Rd
MEET/man/entropy.corrected.Rd
MEET/man/classMODEL.Rd
MEET/man/Hmemory.Rd
MEET/man/missing.fun.Rd
MEET/man/ModelDivergence.Rd
MEET/man/numericalTF.Rd
MEET/man/RattusEntropy.Rd
MEET/man/detection.Rd
MEET/man/align.MEME.Rd
MEET/man/QtoJackson.Rd
MEET/man/MusQresiduals.Rd
MEET/man/PredictPCA.Rd
MEET/man/kfold.Divergence.Rd
MEET/man/probability.Rd
MEET/man/ROCmodel.Rd
MEET/man/CalculPSSM.Rd
MEET/man/ModeltransMEME.Rd
MEET/man/MusDivergence.Rd
MEET/man/detector_1rOrdre_diff.Rd