MEET: MEET: Motif Elements Estimation Toolkit

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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).

Author
Joan Maynou and Erola Pairo.
Date of publication
2013-02-22 16:07:16
Maintainer
Joan Maynou <joan.maynou@upc.edu>
License
GPL (>= 2)
Version
5.1.1

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