Global functions | |
---|---|
.TAXIDToSpecies | Source code |
.create_tables | Source code |
.fillDBOptsWithDefaults | Source code |
.fixTAXID | Source code |
.get_IDlist_by_query | Source code |
.get_Matrix_by_int_id | Source code |
.get_internal_id | Source code |
.get_latest_version | Source code |
.is_latest_version | Source code |
.processJASPARText | Source code |
.store_matrix | Source code |
.store_matrix_acc | Source code |
.store_matrix_annotation | Source code |
.store_matrix_data | Source code |
.store_matrix_species | Source code |
ICMatrix | Man page Source code |
ICMatrix-class | Man page |
ICMatrixList | Man page Source code |
ICMatrixList-class | Man page |
ID | Man page |
ID,XMatrix-method | Man page |
ID,XMatrixList-method | Man page |
ID<-,XMatrix-method | Man page |
IUPAC2Matrix | Man page Source code |
MA0003.2 | Man page |
MA0004.1 | Man page |
MA0043 | Man page |
MA0048 | Man page |
MEME | Source code |
Matrix | Man page |
Matrix,XMatrix-method | Man page |
Matrix,XMatrixList-method | Man page |
Matrix<- | Man page |
Matrix<-,XMatrix-method | Man page |
Motif | Source code |
MotifSet | Man page Source code |
MotifSet-class | Man page |
PFMSimilarity | Man page |
PFMSimilarity,PFMatrix,PFMatrix-method | Man page |
PFMSimilarity,PFMatrix,character-method | Man page |
PFMSimilarity,PFMatrix,matrix-method | Man page |
PFMSimilarity,PFMatrixList,PFMatrix-method | Man page |
PFMSimilarity,PFMatrixList,character-method | Man page |
PFMSimilarity,PFMatrixList,matrix-method | Man page |
PFMSimilarity,matrix,PFMatrix-method | Man page |
PFMSimilarity,matrix,character-method | Man page |
PFMSimilarity,matrix,matrix-method | Man page |
PFMSimilarity-methods | Man page |
PFMatrix | Man page Source code |
PFMatrix-class | Man page |
PFMatrixList | Man page Source code |
PFMatrixList-class | Man page |
PWMEuclidean | Source code |
PWMKL | Source code |
PWMPearson | Source code |
PWMSimilarity | Man page |
PWMSimilarity,PWMatrix,PWMatrix-method | Man page |
PWMSimilarity,PWMatrix,matrix-method | Man page |
PWMSimilarity,PWMatrixList,PWMatrix-method | Man page |
PWMSimilarity,PWMatrixList,PWMatrixList-method | Man page |
PWMSimilarity,PWMatrixList,matrix-method | Man page |
PWMSimilarity,matrix,PWMatrix-method | Man page |
PWMSimilarity,matrix,matrix-method | Man page |
PWMSimilarity-methods | Man page |
PWMatrix | Man page Source code |
PWMatrix-class | Man page |
PWMatrixList | Man page Source code |
PWMatrixList-class | Man page |
PWMrandomizeBayes | Source code |
PWMscore | Source code |
SitePairSet | Man page Source code |
SitePairSet-class | Man page |
SitePairSetList | Man page Source code |
SitePairSetList-class | Man page |
SiteSet | Man page Source code |
SiteSet-class | Man page |
SiteSetList | Man page Source code |
SiteSetList-class | Man page |
TFBSTools | Man page |
TFFM | Man page |
TFFMDetail | Man page Source code |
TFFMFirst | Man page Source code |
XMatrix | Man page |
XMatrix-class | Man page |
XMatrixList | Man page |
XMatrixList,list-method | Man page |
[,MotifSet,ANY,ANY,ANY-method | Man page |
[,MotifSet,ANY,ANY-method | Man page |
[,MotifSet-method | Man page |
[,SiteSet,ANY,ANY,ANY-method | Man page |
[,SiteSet,ANY,ANY-method | Man page |
[,SiteSet-method | Man page |
[-methods | Man page |
addLetter | Source code |
as.data.frame,SitePairSet-method | Man page |
as.data.frame,SitePairSetList-method | Man page |
as.data.frame,SiteSet-method | Man page |
as.data.frame,SiteSetList-method | Man page |
as.matrix,XMatrix-method | Man page |
bg | Man page |
bg,XMatrix-method | Man page |
bg,XMatrixList-method | Man page |
bg<-,XMatrix-method | Man page |
c,SiteSet-method | Man page |
c-methods | Man page |
calConservation | Man page |
calConservation,DNAString,DNAString-method | Man page |
calConservation,DNAStringSet,missing-method | Man page |
calConservation,character,character-method | Man page |
calConservation,character,missing-method | Man page |
calConservation-methods | Man page |
calculate_conservation | Source code |
colSums,XMatrix-method | Man page |
compareMatrix | Source code |
consensusMatrix,MotifSet-method | Man page |
deleteMatrixHavingID | Man page |
deleteMatrixHavingID,JASPAR2014-method | Man page |
deleteMatrixHavingID,JASPAR2016-method | Man page |
deleteMatrixHavingID,JASPAR2018-method | Man page |
deleteMatrixHavingID,JASPAR2020-method | Man page |
deleteMatrixHavingID,JASPAR2022-method | Man page |
deleteMatrixHavingID,SQLiteConnection-method | Man page |
deleteMatrixHavingID,character-method | Man page |
dim,XMatrix-method | Man page |
dirichletMixtureEMEstimation | Source code |
dmmEM | Man page |
dmmEM,ANY-method | Man page |
dmmEM,PFMatrixList-method | Man page |
dmmEM,matrix-method | Man page |
dmmEM-methods | Man page |
do_PairBSgenomeSearch | Source code |
do_PairBSgenomeSearchNegative | Source code |
do_PairBSgenomeSearchNew | Source code |
do_PairBSgenomeSearchPositive | Source code |
do_sitesearch | Source code |
do_sitesearchOneStrand | Source code |
end,SiteSet-method | Man page |
findLargestOverlaps | Source code |
getEmissionProb | Man page |
getEmissionProb,TFFMDetail-method | Man page |
getEmissionProb,TFFMFirst-method | Man page |
getMatrixByID | Man page |
getMatrixByID,JASPAR2014-method | Man page |
getMatrixByID,JASPAR2016-method | Man page |
getMatrixByID,JASPAR2018-method | Man page |
getMatrixByID,JASPAR2020-method | Man page |
getMatrixByID,JASPAR2022-method | Man page |
getMatrixByID,SQLiteConnection-method | Man page |
getMatrixByID,character-method | Man page |
getMatrixByName | Man page |
getMatrixByName,JASPAR2014-method | Man page |
getMatrixByName,JASPAR2016-method | Man page |
getMatrixByName,JASPAR2018-method | Man page |
getMatrixByName,JASPAR2020-method | Man page |
getMatrixByName,JASPAR2022-method | Man page |
getMatrixByName,SQLiteConnection-method | Man page |
getMatrixByName,character-method | Man page |
getMatrixSet | Man page |
getMatrixSet,JASPAR2014-method | Man page |
getMatrixSet,JASPAR2016-method | Man page |
getMatrixSet,JASPAR2018-method | Man page |
getMatrixSet,JASPAR2020-method | Man page |
getMatrixSet,JASPAR2022-method | Man page |
getMatrixSet,SQLiteConnection-method | Man page |
getMatrixSet,character-method | Man page |
getPosProb | Man page |
getPosProb,TFFMDetail-method | Man page |
getPosProb,TFFMFirst-method | Man page |
initializeJASPARDB | Man page |
initializeJASPARDB,JASPAR2014-method | Man page |
initializeJASPARDB,JASPAR2016-method | Man page |
initializeJASPARDB,JASPAR2018-method | Man page |
initializeJASPARDB,JASPAR2020-method | Man page |
initializeJASPARDB,JASPAR2022-method | Man page |
initializeJASPARDB,SQLiteConnection-method | Man page |
initializeJASPARDB,character-method | Man page |
length,MotifSet-method | Man page |
length,SitePairSet-method | Man page |
length,SiteSet-method | Man page |
length,XMatrix-method | Man page |
length-methods | Man page |
letterA | Source code |
letterC | Source code |
letterG | Source code |
letterT | Source code |
makeFlatFileDir | Man page Source code |
matrixClass | Man page |
matrixClass,XMatrix-method | Man page |
matrixClass,XMatrixList-method | Man page |
matrixClass<-,XMatrix-method | Man page |
matrixType | Man page |
matrixType,ICMatrix-method | Man page |
matrixType,PFMatrix-method | Man page |
matrixType,PWMatrix-method | Man page |
matrixType,XMatrixList-method | Man page |
matrixType-methods | Man page |
my.searchSeq | Source code |
name | Man page |
name,XMatrix-method | Man page |
name,XMatrixList-method | Man page |
name<-,XMatrix-method | Man page |
ncol,TFFMDetail-method | Man page |
ncol,TFFMFirst-method | Man page |
ncol,XMatrix-method | Man page |
normargPfm | Source code |
normargPriorParams | Source code |
normargPwm | Source code |
parseMEMEOutput | Man page Source code |
parseMEMEOutput412 | Source code |
pattern,SiteSet-method | Man page |
permuteMatrix | Man page |
permuteMatrix,PFMatrix-method | Man page |
permuteMatrix,PFMatrixList-method | Man page |
permuteMatrix,matrix-method | Man page |
permuteMatrix-methods | Man page |
primary,SiteSet-method | Man page |
pvalues | Man page |
pvalues,SiteSet-method | Man page |
pvalues,SiteSetList-method | Man page |
rPWMDmm | Man page |
rPWMDmm,PFMatrix-method | Man page |
rPWMDmm,PFMatrixList-method | Man page |
rPWMDmm,matrix-method | Man page |
rPWMDmm-methods | Man page |
readJASPARMatrix | Man page Source code |
readMEME | Source code |
readXMLTFFM | Man page Source code |
relScore | Man page |
relScore,SiteSet-method | Man page |
relScore,SiteSetList-method | Man page |
repmat | Source code |
reverseComplement,XMatrix-method | Man page |
rowSums,XMatrix-method | Man page |
runMEME | Man page |
runMEME,DNAStringSet-method | Man page |
runMEME,character-method | Man page |
run_MEME | Source code |
sampleRanges | Man page Source code |
sampleRangesOneStrand | Source code |
schneider_Hnb_approx | Source code |
schneider_Hnb_exact | Source code |
schneider_Hnb_precomputed | Source code |
schneider_correction | Source code |
score,SiteSet-method | Man page |
searchAln | Man page |
searchAln,PWMatrix,Axt,missing-method | Man page |
searchAln,PWMatrix,DNAString,DNAString-method | Man page |
searchAln,PWMatrix,DNAStringSet,missing-method | Man page |
searchAln,PWMatrix,PairwiseAlignmentTFBS,missing-method | Man page |
searchAln,PWMatrix,character,character-method | Man page |
searchAln,PWMatrix,character,missing-method | Man page |
searchAln,PWMatrixList,DNAString,DNAString-method | Man page |
searchAln,PWMatrixList,DNAStringSet,missing-method | Man page |
searchAln,PWMatrixList,PairwiseAlignmentTFBS,missing-method | Man page |
searchAln,PWMatrixList,character,character-method | Man page |
searchAln,PWMatrixList,character,missing-method | Man page |
searchPairBSgenome | Man page |
searchPairBSgenome,PWMatrix-method | Man page |
searchPairBSgenome,PWMatrixList-method | Man page |
searchPairBSgenome-methods | Man page |
searchSeq | Man page |
searchSeq,PWMatrix-method | Man page |
searchSeq,PWMatrixList-method | Man page |
searchSeq-methods | Man page |
seqLogo | Man page |
seqLogo,ICMatrix-method | Man page |
seqLogo,TFFM-method | Man page |
seqLogoTFFM | Source code |
seqname,SiteSet-method | Man page |
shannon.entropy | Man page Source code |
show,SiteSet-method | Man page |
showAsCell,XMatrixList-method | Man page |
site1,SitePairSet-method | Man page |
site2,SitePairSet-method | Man page |
sitesSeq | Man page |
sitesSeq,MotifSet-method | Man page |
sitesource,SiteSet-method | Man page |
start,SiteSet-method | Man page |
storeMatrix | Man page |
storeMatrix,JASPAR2014,PFMatrix-method | Man page |
storeMatrix,JASPAR2014,PFMatrixList-method | Man page |
storeMatrix,JASPAR2016,PFMatrix-method | Man page |
storeMatrix,JASPAR2016,PFMatrixList-method | Man page |
storeMatrix,JASPAR2018,PFMatrix-method | Man page |
storeMatrix,JASPAR2018,PFMatrixList-method | Man page |
storeMatrix,JASPAR2020,PFMatrix-method | Man page |
storeMatrix,JASPAR2020,PFMatrixList-method | Man page |
storeMatrix,JASPAR2022,PFMatrix-method | Man page |
storeMatrix,JASPAR2022,PFMatrixList-method | Man page |
storeMatrix,SQLiteConnection,PFMatrix-method | Man page |
storeMatrix,SQLiteConnection,PFMatrixList-method | Man page |
storeMatrix,character,PFMatrix-method | Man page |
storeMatrix,character,PFMatrixList-method | Man page |
storeMatrix-methods | Man page |
strand,SiteSet-method | Man page |
strand,XMatrix-method | Man page |
strand,XMatrixList-method | Man page |
strand<-,XMatrix-method | Man page |
tags | Man page |
tags,XMatrix-method | Man page |
tags,XMatrixList-method | Man page |
tfbsEnrichment | Source code |
toGRangesList | Man page |
toGRangesList,SitePairSetList,Axt-method | Man page |
toGRangesList-methods | Man page |
toICM | Man page |
toICM,DNAStringSet-method | Man page |
toICM,PFMatrix-method | Man page |
toICM,PFMatrixList-method | Man page |
toICM,character-method | Man page |
toICM,matrix-method | Man page |
toPWM | Man page |
toPWM,DNAStringSet-method | Man page |
toPWM,PFMatrix-method | Man page |
toPWM,PFMatrixList-method | Man page |
toPWM,character-method | Man page |
toPWM,matrix-method | Man page |
totalIC | Man page |
totalIC,ICMatrix-method | Man page |
totalIC,TFFM-method | Man page |
totalIC-methods | Man page |
views | Man page |
views,SiteSet-method | Man page |
writeGFF2 | Man page |
writeGFF2,SitePairSet-method | Man page |
writeGFF2,SitePairSetList-method | Man page |
writeGFF2,SiteSet-method | Man page |
writeGFF2,SiteSetList-method | Man page |
writeGFF2-methods | Man page |
writeGFF3 | Man page |
writeGFF3,SitePairSet-method | Man page |
writeGFF3,SitePairSetList-method | Man page |
writeGFF3,SiteSet-method | Man page |
writeGFF3,SiteSetList-method | Man page |
writeGFF3-methods | Man page |
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