Entry: addCon
Aliases: addCon
Keywords: misc
Description: Add constraints to an already existing constraint set
URL: ../../../library/cosmo/html/addCon.html

Entry: align-class
Aliases: align-class summary,align-method print,align-method show,align-method
Keywords: classes
Description: Class "align"
URL: ../../../library/cosmo/html/align-class.html

Entry: bfile2tmat
Aliases: bfile2tmat
Keywords: 
Description: Converting a MEME-style background file to a transition matrix
URL: ../../../library/cosmo/html/bfile2tmat.html

Entry: bgModel
Aliases: bgModel
Keywords: 
Description: Estimating the background Markov model
URL: ../../../library/cosmo/html/bgModel.html

Entry: boundCon-class
Aliases: boundCon-class boundCon
Keywords: classes
Description: Class "boundCon" ~~~
URL: ../../../library/cosmo/html/boundCon-class.html

Entry: constraintSet-class
Aliases: constraintSet-class plot,constraintSet-method print,constraintSet-method show,constraintSet-method
Keywords: classes
Description: Class "constraintSet" ~~~
URL: ../../../library/cosmo/html/constraintSet-class.html

Entry: cosmo-class
Aliases: cosmo-class plot,cosmo-method summary,cosmo-method print,cosmo-method show,cosmo-method
Keywords: classes
Description: Class "cosmo"
URL: ../../../library/cosmo/html/cosmo-class.html

Entry: cosmo
Aliases: cosmo
Keywords: misc
Description: Constrained motif detection main function
URL: ../../../library/cosmo/html/cosmo.html

Entry: intInfo-class
Aliases: intInfo-class intInfo plot,intInfo-method
Keywords: classes
Description: Class "intInfo" ~~~
URL: ../../../library/cosmo/html/intInfo-class.html

Entry: license.cosmo
Aliases: license.cosmo
Keywords: misc
Description: Print cosmo license
URL: ../../../library/cosmo/html/license.cosmo.html

Entry: makeBoundCon
Aliases: makeBoundCon
Keywords: misc
Description: Constructing a bound constraint
URL: ../../../library/cosmo/html/makeBoundCon.html

Entry: makeConSet
Aliases: makeConSet
Keywords: misc
Description: Constructing a constraint set.
URL: ../../../library/cosmo/html/makeConSet.html

Entry: makePalCon
Aliases: makePalCon
Keywords: misc
Description: Constructing a palindromic constraint
URL: ../../../library/cosmo/html/makePalCon.html

Entry: makePosFreqCon
Aliases: makePosFreqCon
Keywords: misc
Description: Constructing a nucleotide frequency constraint
URL: ../../../library/cosmo/html/makePosFreqCon.html

Entry: makeShapeCon
Aliases: makeShapeCon
Keywords: misc
Description: Constructing a shape constraint
URL: ../../../library/cosmo/html/makeShapeCon.html

Entry: makeShapeDiffCon
Aliases: makeShapeDiffCon
Keywords: misc
Description: Constructing a shape parameter difference constraint
URL: ../../../library/cosmo/html/makeShapeDiffCon.html

Entry: makeSubMotifCon
Aliases: makeSubMotifCon
Keywords: misc
Description: Constructing a submotif constraint
URL: ../../../library/cosmo/html/makeSubMotifCon.html

Entry: motifPWM
Aliases: motifPWM
Keywords: datasets
Description: Example position weight matrix
URL: ../../../library/cosmo/html/motifPWM.html

Entry: palCon-class
Aliases: palCon-class palCon
Keywords: classes
Description: Class "palCon" ~~~
URL: ../../../library/cosmo/html/palCon-class.html

Entry: posFreqCon-class
Aliases: posFreqCon-class posFreqCon
Keywords: classes
Description: Class "posFreqCon" ~~~
URL: ../../../library/cosmo/html/posFreqCon-class.html

Entry: postProbs-class
Aliases: postProbs-class plot,postProbs-method
Keywords: classes
Description: Class "postProbs"
URL: ../../../library/cosmo/html/postProbs-class.html

Entry: readConFile
Aliases: readConFile
Keywords: misc
Description: Reads in a constraint file.
URL: ../../../library/cosmo/html/readConFile.html

Entry: rseq
Aliases: rseq
Keywords: misc
Description: Random generation of DNA sequence according to ZOOPS or TCM model
URL: ../../../library/cosmo/html/rseq.html

Entry: shapeCon-class
Aliases: shapeCon-class shapeCon
Keywords: classes
Description: Class "shapeCon" ~~~
URL: ../../../library/cosmo/html/shapeCon-class.html

Entry: shapeDiffCon-class
Aliases: shapeDiffCon-class shapeDiffCon
Keywords: classes
Description: Class "shapeDiffCon" ~~~
URL: ../../../library/cosmo/html/shapeDiffCon-class.html

Entry: simScore
Aliases: simScore
Keywords: misc
Description: Score motif detection simulation results
URL: ../../../library/cosmo/html/simScore.html

Entry: subMotifCon-class
Aliases: subMotifCon subMotifCon-class
Keywords: classes
Description: Class "subMotifCon" ~~~
URL: ../../../library/cosmo/html/subMotifCon-class.html

Entry: transMats
Aliases: transMats
Keywords: datasets
Description: Example transition matrix in list format
URL: ../../../library/cosmo/html/transMats.html

Entry: writeConFile
Aliases: writeConFile
Keywords: misc
Description: Converts an object of class 'constraintSet' into a text file
URL: ../../../library/cosmo/html/writeConFile.html
