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| addCon | Add constraints to an already existing constraint set |
| align-class | Class "align" |
| bfile2tmat | Converting a MEME-style background file to a transition matrix |
| bgModel | Estimating the background Markov model |
| boundCon | Class "boundCon" ~~~ |
| boundCon-class | Class "boundCon" ~~~ |
| constraintSet-class | Class "constraintSet" ~~~ |
| cosmo | Constrained motif detection main function |
| cosmo-class | Class "cosmo" |
| intInfo | Class "intInfo" ~~~ |
| intInfo-class | Class "intInfo" ~~~ |
| license.cosmo | Print cosmo license |
| makeBoundCon | Constructing a bound constraint |
| makeConSet | Constructing a constraint set. |
| makePalCon | Constructing a palindromic constraint |
| makePosFreqCon | Constructing a nucleotide frequency constraint |
| makeShapeCon | Constructing a shape constraint |
| makeShapeDiffCon | Constructing a shape parameter difference constraint |
| makeSubMotifCon | Constructing a submotif constraint |
| motifPWM | Example position weight matrix |
| palCon | Class "palCon" ~~~ |
| palCon-class | Class "palCon" ~~~ |
| plot,constraintSet-method | Class "constraintSet" ~~~ |
| plot,cosmo-method | Class "cosmo" |
| plot,intInfo-method | Class "intInfo" ~~~ |
| plot,postProbs-method | Class "postProbs" |
| posFreqCon | Class "posFreqCon" ~~~ |
| posFreqCon-class | Class "posFreqCon" ~~~ |
| postProbs-class | Class "postProbs" |
| print,align-method | Class "align" |
| print,constraintSet-method | Class "constraintSet" ~~~ |
| print,cosmo-method | Class "cosmo" |
| readConFile | Reads in a constraint file. |
| rseq | Random generation of DNA sequence according to ZOOPS or TCM model |
| shapeCon | Class "shapeCon" ~~~ |
| shapeCon-class | Class "shapeCon" ~~~ |
| shapeDiffCon | Class "shapeDiffCon" ~~~ |
| shapeDiffCon-class | Class "shapeDiffCon" ~~~ |
| show,align-method | Class "align" |
| show,constraintSet-method | Class "constraintSet" ~~~ |
| show,cosmo-method | Class "cosmo" |
| simScore | Score motif detection simulation results |
| subMotifCon | Class "subMotifCon" ~~~ |
| subMotifCon-class | Class "subMotifCon" ~~~ |
| summary,align-method | Class "align" |
| summary,cosmo-method | Class "cosmo" |
| transMats | Example transition matrix in list format |
| writeConFile | Converts an object of class 'constraintSet' into a text file |