Man pages for ge11232002/TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
| calConservation-methods | calConservation method |
| deleteMatrixHavingID-methods | JASPAR database operations |
| dmmEM-methods | dmmEM method |
| getEmissionProb | Get the emission distribution parameters. |
| getMatrixByID-methods | Basic JASPAR database search functionis 'getMatrixByID',... |
| getMatrixSet-methods | Advanced JASPAR database search functions 'get_MatrixSet' |
| getPosProb | Get the emission probabilities of nucleotides |
| IUPAC2Matrix | IUPAC2Matrix |
| MA0004.1 | Some example PFM matrices. |
| makeFlatFileDir | Generate "FlatFileDir" directory |
| MotifSet-class | Class '"MotifSet"' |
| parseMEMEOutput | parseMEMEOutput |
| permuteMatrix-methods | permuteMatrix method |
| PFMSimilarity-methods | PFMSimilarity method |
| PWMSimilarity-methods | PWMSimilarity method |
| readJASPARMatrix | Read JASPAR format matrix |
| readXMLTFFM | readXMLTFFM |
| rPWMDmm-methods | rPWMDmm method |
| runMEME-methods | Wrapper function for MEME |
| sampleRanges | sampleRanges |
| searchAln-methods | searchAln method |
| searchPairBSgenome-methods | searchPairBSgenome method |
| searchSeq-methods | searchSeq method |
| seqLogo | Plot a sequence logo |
| shannon.entropy | Calculate the Shannon entropy |
| SitePairSet-class | Class '"SitePairSet"' |
| SitePairSetList-class | Class '"SitePairSetList"' |
| SiteSet-class | Class '"SiteSet"' |
| SiteSetList-class | Class '"SiteSetList"' |
| TFBSTools-package | TFBS software package. |
| TFFM-class | The TFFM class |
| toGRangesList-methods | toGRangesList function |
| toICM-methods | toICM method |
| toPWM-methods | toPWM method |
| writeGFF3-methods | 'writeGFF3', 'writeGFF2' functions |
| XMatrix-class | '"XMatrix"' objects |
| XMatrixList-class | Class '"XMatrixList"' |
