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-method | Class "constraintSet" ~~~ |
plot-method | Class "cosmo" |
plot-method | Class "intInfo" ~~~ |
plot-method | Class "postProbs" |
posFreqCon | Class "posFreqCon" ~~~ |
posFreqCon-class | Class "posFreqCon" ~~~ |
postProbs-class | Class "postProbs" |
print-method | Class "align" |
print-method | Class "constraintSet" ~~~ |
print-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-method | Class "align" |
show-method | Class "constraintSet" ~~~ |
show-method | Class "cosmo" |
simScore | Score motif detection simulation results |
subMotifCon | Class "subMotifCon" ~~~ |
subMotifCon-class | Class "subMotifCon" ~~~ |
summary-method | Class "align" |
summary-method | Class "cosmo" |
transMats | Example transition matrix in list format |
writeConFile | Converts an object of class 'constraintSet' into a text file |