Package: TFBSTools 1.45.1
Ge Tan
TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
Authors:
TFBSTools_1.45.1.tar.gz
TFBSTools_1.45.0.zip(r-4.5)TFBSTools_1.45.0.zip(r-4.4)TFBSTools_1.45.0.zip(r-4.3)
TFBSTools_1.45.1.tgz(r-4.4-x86_64)TFBSTools_1.45.1.tgz(r-4.4-arm64)TFBSTools_1.45.1.tgz(r-4.3-x86_64)TFBSTools_1.45.1.tgz(r-4.3-arm64)
TFBSTools_1.45.1.tar.gz(r-4.5-noble)TFBSTools_1.45.1.tar.gz(r-4.4-noble)
TFBSTools_1.45.1.tgz(r-4.4-emscripten)
TFBSTools.pdf |TFBSTools.html✨
TFBSTools/json (API)
NEWS
| # Install 'TFBSTools' in R: |
| install.packages('TFBSTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ge11232002/tfbstools/issues
On BioConductor:TFBSTools-1.45.0(bioc 3.21)TFBSTools-1.44.0(bioc 3.20)
motifannotationgeneregulationmotifdiscoverytranscriptionalignment
Last updated 3 days agofrom:2c2776b6c7. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 25 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 27 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 25 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 27 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 25 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 25 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 27 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 25 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 25 2024 |
Exports:as.data.frameas.matrixbgcalConservationcolSumsconsensusMatrixdeleteMatrixHavingIDdmmEMendgetEmissionProbgetMatrixByIDgetMatrixByNamegetMatrixSetgetPosProbICMatrixICMatrixListIDinitializeJASPARDBIUPAC2MatrixmakeFlatFileDirMatrixMatrix<-matrixClassmatrixTypeMotifSetnamencolparseMEMEOutputpermuteMatrixPFMatrixPFMatrixListPFMSimilaritypvaluesPWMatrixPWMatrixListPWMSimilarityreadJASPARMatrixreadXMLTFFMrelScorereverseComplementrowSumsrPWMDmmrunMEMEsampleRangessearchAlnsearchPairBSgenomesearchSeqseqLogoshannon.entropyshowAsCellSitePairSetSitePairSetListSiteSetSiteSetListsitesSeqstartstoreMatrixtagsTFFMDetailTFFMFirsttoGRangesListtoICMtoPWMtotalICviewswriteGFF2writeGFF3XMatrixList
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolsclicliprCNErcodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDirichletMultinomialfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2glueGO.dbgtablegtoolshmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogresspwalignR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesseqLogosnowSparseArraystringistringrSummarizedExperimentsysTFMPvaluetibbletidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| TFBS software package. | TFBSTools |
| calConservation method | calConservation calConservation,character,character-method calConservation,character,missing-method calConservation,DNAString,DNAString-method calConservation,DNAStringSet,missing-method calConservation-methods |
| JASPAR database operations | deleteMatrixHavingID deleteMatrixHavingID,character-method deleteMatrixHavingID,JASPAR2014-method deleteMatrixHavingID,JASPAR2016-method deleteMatrixHavingID,JASPAR2018-method deleteMatrixHavingID,JASPAR2020-method deleteMatrixHavingID,JASPAR2022-method deleteMatrixHavingID,SQLiteConnection-method initializeJASPARDB initializeJASPARDB,character-method initializeJASPARDB,JASPAR2014-method initializeJASPARDB,JASPAR2016-method initializeJASPARDB,JASPAR2018-method initializeJASPARDB,JASPAR2020-method initializeJASPARDB,JASPAR2022-method initializeJASPARDB,SQLiteConnection-method storeMatrix storeMatrix,character,PFMatrix-method storeMatrix,character,PFMatrixList-method storeMatrix,JASPAR2014,PFMatrix-method storeMatrix,JASPAR2014,PFMatrixList-method storeMatrix,JASPAR2016,PFMatrix-method storeMatrix,JASPAR2016,PFMatrixList-method storeMatrix,JASPAR2018,PFMatrix-method storeMatrix,JASPAR2018,PFMatrixList-method storeMatrix,JASPAR2020,PFMatrix-method storeMatrix,JASPAR2020,PFMatrixList-method storeMatrix,JASPAR2022,PFMatrix-method storeMatrix,JASPAR2022,PFMatrixList-method storeMatrix,SQLiteConnection,PFMatrix-method storeMatrix,SQLiteConnection,PFMatrixList-method storeMatrix-methods |
| dmmEM method | dmmEM dmmEM,ANY-method dmmEM,matrix-method dmmEM,PFMatrixList-method dmmEM-methods |
| Get the emission distribution parameters. | getEmissionProb getEmissionProb,TFFMDetail-method getEmissionProb,TFFMFirst-method |
| Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName' | getMatrixByID getMatrixByID,character-method getMatrixByID,JASPAR2014-method getMatrixByID,JASPAR2016-method getMatrixByID,JASPAR2018-method getMatrixByID,JASPAR2020-method getMatrixByID,JASPAR2022-method getMatrixByID,SQLiteConnection-method getMatrixByName getMatrixByName,character-method getMatrixByName,JASPAR2014-method getMatrixByName,JASPAR2016-method getMatrixByName,JASPAR2018-method getMatrixByName,JASPAR2020-method getMatrixByName,JASPAR2022-method getMatrixByName,SQLiteConnection-method |
| Advanced JASPAR database search functions 'get_MatrixSet' | getMatrixSet getMatrixSet,character-method getMatrixSet,JASPAR2014-method getMatrixSet,JASPAR2016-method getMatrixSet,JASPAR2018-method getMatrixSet,JASPAR2020-method getMatrixSet,JASPAR2022-method getMatrixSet,SQLiteConnection-method |
| Get the emission probabilities of nucleotides | getPosProb getPosProb,TFFMDetail-method getPosProb,TFFMFirst-method |
| IUPAC2Matrix | IUPAC2Matrix |
| Some example PFM matrices. | MA0003.2 MA0004.1 MA0043 MA0048 |
| Generate "FlatFileDir" directory | makeFlatFileDir |
| Class '"MotifSet"' | consensusMatrix,MotifSet-method length,MotifSet-method MotifSet MotifSet-class sitesSeq sitesSeq,MotifSet-method [,MotifSet,ANY,ANY,ANY-method [,MotifSet,ANY,ANY-method [,MotifSet-method |
| parseMEMEOutput | parseMEMEOutput |
| permuteMatrix method | permuteMatrix permuteMatrix,matrix-method permuteMatrix,PFMatrix-method permuteMatrix,PFMatrixList-method permuteMatrix-methods |
| PFMSimilarity method | PFMSimilarity PFMSimilarity,matrix,character-method PFMSimilarity,matrix,matrix-method PFMSimilarity,matrix,PFMatrix-method PFMSimilarity,PFMatrix,character-method PFMSimilarity,PFMatrix,matrix-method PFMSimilarity,PFMatrix,PFMatrix-method PFMSimilarity,PFMatrixList,character-method PFMSimilarity,PFMatrixList,matrix-method PFMSimilarity,PFMatrixList,PFMatrix-method PFMSimilarity-methods |
| PWMSimilarity method | PWMSimilarity PWMSimilarity,matrix,matrix-method PWMSimilarity,matrix,PWMatrix-method PWMSimilarity,PWMatrix,matrix-method PWMSimilarity,PWMatrix,PWMatrix-method PWMSimilarity,PWMatrixList,matrix-method PWMSimilarity,PWMatrixList,PWMatrix-method PWMSimilarity,PWMatrixList,PWMatrixList-method PWMSimilarity-methods |
| Read JASPAR format matrix | readJASPARMatrix |
| readXMLTFFM | readXMLTFFM |
| rPWMDmm method | rPWMDmm rPWMDmm,matrix-method rPWMDmm,PFMatrix-method rPWMDmm,PFMatrixList-method rPWMDmm-methods |
| Wrapper function for MEME | runMEME runMEME,character-method runMEME,DNAStringSet-method |
| sampleRanges | sampleRanges |
| searchAln method | searchAln searchAln,PWMatrix,Axt,missing-method searchAln,PWMatrix,character,character-method searchAln,PWMatrix,character,missing-method searchAln,PWMatrix,DNAString,DNAString-method searchAln,PWMatrix,DNAStringSet,missing-method searchAln,PWMatrixList,character,character-method searchAln,PWMatrixList,character,missing-method searchAln,PWMatrixList,DNAString,DNAString-method searchAln,PWMatrixList,DNAStringSet,missing-method |
| searchPairBSgenome method | searchPairBSgenome searchPairBSgenome,PWMatrix-method searchPairBSgenome,PWMatrixList-method searchPairBSgenome-methods |
| searchSeq method | searchSeq searchSeq,PWMatrix-method searchSeq,PWMatrixList-method searchSeq-methods |
| Plot a sequence logo | seqLogo seqLogo,ICMatrix-method seqLogo,TFFM-method |
| Calculate the Shannon entropy | shannon.entropy |
| Class '"SitePairSet"' | as.data.frame,SitePairSet-method length,SitePairSet-method site1,SitePairSet-method site2,SitePairSet-method SitePairSet SitePairSet-class |
| Class '"SitePairSetList"' | as.data.frame,SitePairSetList-method SitePairSetList SitePairSetList-class |
| Class '"SiteSet"' | as.data.frame,SiteSet-method c,SiteSet-method c-methods end,SiteSet-method length,SiteSet-method pattern,SiteSet-method primary,SiteSet-method pvalues pvalues,SiteSet-method relScore relScore,SiteSet-method score,SiteSet-method seqname,SiteSet-method show,SiteSet-method SiteSet SiteSet-class sitesource,SiteSet-method start,SiteSet-method strand,SiteSet-method views views,SiteSet-method [,SiteSet,ANY,ANY,ANY-method [,SiteSet,ANY,ANY-method [,SiteSet-method |
| Class '"SiteSetList"' | as.data.frame,SiteSetList-method pvalues,SiteSetList-method relScore,SiteSetList-method SiteSetList SiteSetList-class |
| The TFFM class | ncol,TFFMDetail-method ncol,TFFMFirst-method TFFM TFFMDetail TFFMFirst totalIC,TFFM-method |
| toGRangesList function | toGRangesList toGRangesList,SitePairSetList,Axt-method toGRangesList-methods |
| toICM method | toICM toICM,character-method toICM,DNAStringSet-method toICM,matrix-method toICM,PFMatrix-method toICM,PFMatrixList-method |
| toPWM method | toPWM toPWM,character-method toPWM,DNAStringSet-method toPWM,matrix-method toPWM,PFMatrix-method toPWM,PFMatrixList-method |
| 'writeGFF3', 'writeGFF2' functions | writeGFF2 writeGFF2,SitePairSet-method writeGFF2,SitePairSetList-method writeGFF2,SiteSet-method writeGFF2,SiteSetList-method writeGFF2-methods writeGFF3 writeGFF3,SitePairSet-method writeGFF3,SitePairSetList-method writeGFF3,SiteSet-method writeGFF3,SiteSetList-method writeGFF3-methods |
| '"XMatrix"' objects | as.matrix,XMatrix-method bg bg,XMatrix-method bg<-,XMatrix-method colSums,XMatrix-method dim,XMatrix-method ICMatrix ICMatrix-class ID ID,XMatrix-method ID<-,XMatrix-method length,XMatrix-method length-methods Matrix Matrix,XMatrix-method Matrix<- Matrix<-,XMatrix-method matrixClass matrixClass,XMatrix-method matrixClass<-,XMatrix-method matrixType matrixType,ICMatrix-method matrixType,PFMatrix-method matrixType,PWMatrix-method matrixType-methods name name,XMatrix-method name<-,XMatrix-method ncol,XMatrix-method PFMatrix PFMatrix-class PWMatrix PWMatrix-class reverseComplement,XMatrix-method rowSums,XMatrix-method strand,XMatrix-method strand<-,XMatrix-method tags tags,XMatrix-method totalIC totalIC,ICMatrix-method totalIC-methods XMatrix XMatrix-class [-methods |
| Class '"XMatrixList"' | bg,XMatrixList-method ICMatrixList ICMatrixList-class ID,XMatrixList-method Matrix,XMatrixList-method matrixClass,XMatrixList-method matrixType,XMatrixList-method name,XMatrixList-method PFMatrixList PFMatrixList-class PWMatrixList PWMatrixList-class showAsCell,XMatrixList-method strand,XMatrixList-method tags,XMatrixList-method XMatrixList XMatrixList,list-method |
