Software Package for Transcription Factor Binding Site (TFBS)
Analysis
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘TFBSTools’ version 1.47.0
Help Pages
A B C D E G I L M N P R S T V W X misc
-- A --
| 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 |
-- B --
| bg | '"XMatrix"' objects |
| bg-method | '"XMatrix"' objects |
| bg-method | Class '"XMatrixList"' |
| bg<--method | '"XMatrix"' objects |
-- C --
| 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"' |
-- D --
| deleteMatrixHavingID | JASPAR database operations |
| deleteMatrixHavingID-method | JASPAR database operations |
| dim-method | '"XMatrix"' objects |
| dmmEM | dmmEM method |
| dmmEM-method | dmmEM method |
| dmmEM-methods | dmmEM method |
-- E --
| end-method | Class '"SiteSet"' |
-- G --
| 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 |
-- I --
| 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 |
-- L --
| length-method | Class '"MotifSet"' |
| length-method | Class '"SitePairSet"' |
| length-method | Class '"SiteSet"' |
| length-method | '"XMatrix"' objects |
| length-methods | '"XMatrix"' objects |
-- M --
| 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"' |
-- N --
| name | '"XMatrix"' objects |
| name-method | '"XMatrix"' objects |
| name-method | Class '"XMatrixList"' |
| name<--method | '"XMatrix"' objects |
| ncol-method | The TFFM class |
| ncol-method | '"XMatrix"' objects |
-- P --
| 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 |
-- R --
| 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 |
-- S --
| 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 |
-- T --
| 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 |
-- V --
| views | Class '"SiteSet"' |
| views-method | Class '"SiteSet"' |
-- W --
| 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 |
-- X --
| XMatrix | '"XMatrix"' objects |
| XMatrix-class | '"XMatrix"' objects |
| XMatrixList | Class '"XMatrixList"' |
| XMatrixList-method | Class '"XMatrixList"' |
-- misc --
| [-method | Class '"MotifSet"' |
| [-method | Class '"SiteSet"' |
| [-methods | '"XMatrix"' objects |