A B C D E G I L M N P R S T V W X misc
as.data.frame-method | Class '"SitePairSet"' |
as.data.frame-method | Class '"SitePairSetList"' |
as.data.frame-method | Class '"SiteSet"' |
as.data.frame-method | Class '"SiteSetList"' |
as.matrix-method | '"XMatrix"' objects |
bg | '"XMatrix"' objects |
bg-method | '"XMatrix"' objects |
bg-method | Class '"XMatrixList"' |
bg<--method | '"XMatrix"' objects |
c-method | Class '"SiteSet"' |
c-methods | Class '"SiteSet"' |
calConservation | calConservation method |
calConservation-method | calConservation method |
calConservation-methods | calConservation method |
colSums-method | '"XMatrix"' objects |
consensusMatrix-method | Class '"MotifSet"' |
deleteMatrixHavingID | JASPAR database operations |
deleteMatrixHavingID-method | JASPAR database operations |
dim-method | '"XMatrix"' objects |
dmmEM | dmmEM method |
dmmEM-method | dmmEM method |
dmmEM-methods | dmmEM method |
end-method | Class '"SiteSet"' |
getEmissionProb | Get the emission distribution parameters. |
getEmissionProb-method | Get the emission distribution parameters. |
getMatrixByID | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName' |
getMatrixByID-method | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName' |
getMatrixByName | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName' |
getMatrixByName-method | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName' |
getMatrixSet | Advanced JASPAR database search functions 'get_MatrixSet' |
getMatrixSet-method | Advanced JASPAR database search functions 'get_MatrixSet' |
getPosProb | Get the emission probabilities of nucleotides |
getPosProb-method | Get the emission probabilities of nucleotides |
ICMatrix | '"XMatrix"' objects |
ICMatrix-class | '"XMatrix"' objects |
ICMatrixList | Class '"XMatrixList"' |
ICMatrixList-class | Class '"XMatrixList"' |
ID | '"XMatrix"' objects |
ID-method | '"XMatrix"' objects |
ID-method | Class '"XMatrixList"' |
ID<--method | '"XMatrix"' objects |
initializeJASPARDB | JASPAR database operations |
initializeJASPARDB-method | JASPAR database operations |
IUPAC2Matrix | IUPAC2Matrix |
length-method | Class '"MotifSet"' |
length-method | Class '"SitePairSet"' |
length-method | Class '"SiteSet"' |
length-method | '"XMatrix"' objects |
length-methods | '"XMatrix"' objects |
MA0003.2 | Some example PFM matrices. |
MA0004.1 | Some example PFM matrices. |
MA0043 | Some example PFM matrices. |
MA0048 | Some example PFM matrices. |
makeFlatFileDir | Generate "FlatFileDir" directory |
Matrix | '"XMatrix"' objects |
Matrix-method | '"XMatrix"' objects |
Matrix-method | Class '"XMatrixList"' |
Matrix<- | '"XMatrix"' objects |
Matrix<--method | '"XMatrix"' objects |
matrixClass | '"XMatrix"' objects |
matrixClass-method | '"XMatrix"' objects |
matrixClass-method | Class '"XMatrixList"' |
matrixClass<--method | '"XMatrix"' objects |
matrixType | '"XMatrix"' objects |
matrixType-method | '"XMatrix"' objects |
matrixType-method | Class '"XMatrixList"' |
matrixType-methods | '"XMatrix"' objects |
MotifSet | Class '"MotifSet"' |
MotifSet-class | Class '"MotifSet"' |
name | '"XMatrix"' objects |
name-method | '"XMatrix"' objects |
name-method | Class '"XMatrixList"' |
name<--method | '"XMatrix"' objects |
ncol-method | The TFFM class |
ncol-method | '"XMatrix"' objects |
parseMEMEOutput | parseMEMEOutput |
pattern-method | Class '"SiteSet"' |
permuteMatrix | permuteMatrix method |
permuteMatrix-method | permuteMatrix method |
permuteMatrix-methods | permuteMatrix method |
PFMatrix | '"XMatrix"' objects |
PFMatrix-class | '"XMatrix"' objects |
PFMatrixList | Class '"XMatrixList"' |
PFMatrixList-class | Class '"XMatrixList"' |
PFMSimilarity | PFMSimilarity method |
PFMSimilarity-method | PFMSimilarity method |
PFMSimilarity-methods | PFMSimilarity method |
primary-method | Class '"SiteSet"' |
pvalues | Class '"SiteSet"' |
pvalues-method | Class '"SiteSet"' |
pvalues-method | Class '"SiteSetList"' |
PWMatrix | '"XMatrix"' objects |
PWMatrix-class | '"XMatrix"' objects |
PWMatrixList | Class '"XMatrixList"' |
PWMatrixList-class | Class '"XMatrixList"' |
PWMSimilarity | PWMSimilarity method |
PWMSimilarity-method | PWMSimilarity method |
PWMSimilarity-methods | PWMSimilarity method |
readJASPARMatrix | Read JASPAR format matrix |
readXMLTFFM | readXMLTFFM |
relScore | Class '"SiteSet"' |
relScore-method | Class '"SiteSet"' |
relScore-method | Class '"SiteSetList"' |
reverseComplement-method | '"XMatrix"' objects |
rowSums-method | '"XMatrix"' objects |
rPWMDmm | rPWMDmm method |
rPWMDmm-method | rPWMDmm method |
rPWMDmm-methods | rPWMDmm method |
runMEME | Wrapper function for MEME |
runMEME-method | Wrapper function for MEME |
sampleRanges | sampleRanges |
score-method | Class '"SiteSet"' |
searchAln | searchAln method |
searchAln-method | searchAln method |
searchPairBSgenome | searchPairBSgenome method |
searchPairBSgenome-method | searchPairBSgenome method |
searchPairBSgenome-methods | searchPairBSgenome method |
searchSeq | searchSeq method |
searchSeq-method | searchSeq method |
searchSeq-methods | searchSeq method |
seqLogo | Plot a sequence logo |
seqLogo-method | Plot a sequence logo |
seqname-method | Class '"SiteSet"' |
shannon.entropy | Calculate the Shannon entropy |
show-method | Class '"SiteSet"' |
showAsCell-method | Class '"XMatrixList"' |
site1-method | Class '"SitePairSet"' |
site2-method | Class '"SitePairSet"' |
SitePairSet | Class '"SitePairSet"' |
SitePairSet-class | Class '"SitePairSet"' |
SitePairSetList | Class '"SitePairSetList"' |
SitePairSetList-class | Class '"SitePairSetList"' |
SiteSet | Class '"SiteSet"' |
SiteSet-class | Class '"SiteSet"' |
SiteSetList | Class '"SiteSetList"' |
SiteSetList-class | Class '"SiteSetList"' |
sitesource-method | Class '"SiteSet"' |
sitesSeq | Class '"MotifSet"' |
sitesSeq-method | Class '"MotifSet"' |
start-method | Class '"SiteSet"' |
storeMatrix | JASPAR database operations |
storeMatrix-method | JASPAR database operations |
storeMatrix-methods | JASPAR database operations |
strand-method | Class '"SiteSet"' |
strand-method | '"XMatrix"' objects |
strand-method | Class '"XMatrixList"' |
strand<--method | '"XMatrix"' objects |
tags | '"XMatrix"' objects |
tags-method | '"XMatrix"' objects |
tags-method | Class '"XMatrixList"' |
TFBSTools | TFBS software package. |
TFFM | The TFFM class |
TFFMDetail | The TFFM class |
TFFMFirst | The TFFM class |
toGRangesList | toGRangesList function |
toGRangesList-method | toGRangesList function |
toGRangesList-methods | toGRangesList function |
toICM | toICM method |
toICM-method | toICM method |
toPWM | toPWM method |
toPWM-method | toPWM method |
totalIC | '"XMatrix"' objects |
totalIC-method | The TFFM class |
totalIC-method | '"XMatrix"' objects |
totalIC-methods | '"XMatrix"' objects |
views | Class '"SiteSet"' |
views-method | Class '"SiteSet"' |
writeGFF2 | 'writeGFF3', 'writeGFF2' functions |
writeGFF2-method | 'writeGFF3', 'writeGFF2' functions |
writeGFF2-methods | 'writeGFF3', 'writeGFF2' functions |
writeGFF3 | 'writeGFF3', 'writeGFF2' functions |
writeGFF3-method | 'writeGFF3', 'writeGFF2' functions |
writeGFF3-methods | 'writeGFF3', 'writeGFF2' functions |
XMatrix | '"XMatrix"' objects |
XMatrix-class | '"XMatrix"' objects |
XMatrixList | Class '"XMatrixList"' |
XMatrixList-method | Class '"XMatrixList"' |
[-method | Class '"MotifSet"' |
[-method | Class '"SiteSet"' |
[-methods | '"XMatrix"' objects |