Package: motifStack 1.51.0
Jianhong Ou
motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
Authors:
motifStack_1.51.0.tar.gz
motifStack_1.51.0.zip(r-4.5)motifStack_1.51.0.zip(r-4.4)motifStack_1.51.0.zip(r-4.3)
motifStack_1.51.0.tgz(r-4.4-any)motifStack_1.51.0.tgz(r-4.3-any)
motifStack_1.51.0.tar.gz(r-4.5-noble)motifStack_1.51.0.tar.gz(r-4.4-noble)
motifStack_1.51.0.tgz(r-4.4-emscripten)
motifStack.pdf |motifStack.html✨
motifStack/json (API)
NEWS
| # Install 'motifStack' in R: |
| install.packages('motifStack', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:motifStack-1.51.0(bioc 3.21)motifStack-1.50.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport
Last updated 2 months agofrom:29749139df. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | OK | Nov 29 2024 |
| R-4.5-linux | OK | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:AAmotifAlignmentaddBlankas.data.framebrowseMotifsbrowseMotifsOutputclusterMotifscoercecolorsetDNAmotifAlignmentDNAmotifToRNAmotifformatfrequencegeom_motifGeomMotifgetICgetRankedUniqueMotifshighlightColimportMatrixmatalignmatrixReverseComplementmergeMotifsmotifCircosmotifCloudmotifGrobmotifHclustmotifPilesmotifSignaturemotifStacknodelistpcm2pfmpcm2pssmpfm2pwmplotplotAffinityLogoplotMotifLogoplotMotifLogoAplotMotifLogoStackplotMotifLogoStackWithTreeplotMotifOverMotifplotMotifStackWithPhylogplotMotifStackWithRadialPhylogreadPCMrenderbrowseMotifsreorderUPGMAtreesigColorsignaturestrimMotif
Dependencies:abindade4annotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcaToolsclicliprCNErcodetoolscolorspacecpp11crayoncurlDBIDelayedArraydigestDirichletMultinomialevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2glueGO.dbgtablegtoolshighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpixmappkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogresspwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesseqLogosnowspSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot stacked logos for single or multiple DNA, RNA and amino acid sequence | motifStack-package |
| align AA motifs | AAmotifAlignment |
| browse motifs | browseMotifs |
| Shiny bindings for browseMotifs | browseMotifs-shiny browseMotifsOutput renderbrowseMotifs |
| calculate frequence | calF |
| calculate I' | calI |
| cluster motifs | clusterMotifs |
| retrieve color setting for logo | colorset |
| compare two profiles | compare2profiles |
| comapre w pcm | compareProfiles |
| align DNA motifs | DNAmotifAlignment |
| convert DNA motif into RNA motif | DNAmotifToRNAmotif |
| Global alignment version | dpGlobal |
| Dynamic programming function, local version | dpLocal |
| geom_motif | geom_motif |
| GeomMotif object | GeomMotif |
| calculate ALLR from counts | getALLRscoreFromCounts |
| Calculate distances between two profiles | getDistance |
| get the unique motif in each category grouped by distance | getRankedUniqueMotifs |
| Calculate pair_wise position score | getScore |
| add alpha transparency value to a color | highlightCol |
| import motifs from local files | importMatrix |
| Class 'marker' | $,marker-method $<-,marker-method marker marker-class |
| Matrix Aligner | matalign |
| merge multiple motifs | mergeMotifs |
| plot sequence logo stacks with a radial phylogenic tree and multiple color rings | motifCircos |
| plot a DNA sequence logo cloud | motifCloud |
| Motif Grob | motifGrob |
| Hierarchical Clustering motifs | motifHclust |
| plot sequence logo stacks with a linear phylogenic tree and multiple color sets | motifPiles |
| Class '"motifSig"' | $,motifSig-method $<-,motifSig-method frequence frequence,motifSig-method motifSig motifSig-class nodelist nodelist,motifSig-method sigColor sigColor,motifSig-method signatures signatures,motifSig-method |
| get signatures from motifs | motifSignature |
| plot a DNA sequence logo stack | motifStack |
| Class 'ouNode' | $,ouNode-method $<-,ouNode-method ouNode ouNode-class |
| Class '"pcm"' | $,pcm-method $<-,pcm-method addBlank addBlank,pcm,numeric,logical-method as as.data.frame,pcm-method coerce,pcm,matrix-method format,pcm-method getIC getIC,pcm,ANY-method matrixReverseComplement matrixReverseComplement,pcm-method pcm pcm-class pcm2pfm pcm2pfm,data.frame,ANY-method pcm2pfm,data.frame,numeric-method pcm2pfm,list,ANY-method pcm2pfm,list,numeric-method pcm2pfm,matrix,ANY-method pcm2pfm,matrix,numeric-method pcm2pfm,pcm,ANY-method pcm2pssm pcm2pssm,data.frame,ANY-method pcm2pssm,data.frame,numeric-method pcm2pssm,list,ANY-method pcm2pssm,list,numeric-method pcm2pssm,matrix,ANY-method pcm2pssm,matrix,numeric-method pcm2pssm,pcm,ANY-method plot plot,pcm,ANY-method trimMotif trimMotif,pcm,numeric-method |
| Class '"pfm"' | $,pfm-method $<-,pfm-method addBlank,pfm,numeric,logical-method as.data.frame,pfm-method coerce coerce,pfm,matrix-method format,pfm-method getIC,matrix,matrix-method getIC,matrix,numeric-method getIC,pfm,ANY-method matrixReverseComplement,pfm-method pfm pfm-class plot,pfm,ANY-method trimMotif,pfm,numeric-method |
| convert pfm object to PWM | pfm2pwm |
| plot affinity logo | plotAffinityLogo |
| plot sequence logo | plotMotifLogo |
| plot sequence logo without plot.new | plotMotifLogoA |
| plot sequence logos stack | plotMotifLogoStack |
| plot sequence logos stack with hierarchical cluster tree | plotMotifLogoStackWithTree |
| plot motif over another motif | plotMotifOverMotif |
| plot sequence logo stacks with a ape4-style phylogenic tree | plotMotifStackWithPhylog |
| plot sequence logo stacks with a radial phylogenic tree | plotMotifStackWithRadialPhylog |
| plot x-axis | plotXaxis |
| plot y-axis | plotYaxis |
| Class '"psam"' | $,psam-method $<-,psam-method addBlank,psam,numeric,logical-method as() as.data.frame,psam-method coerce,psam,matrix-method format,psam-method matrixReverseComplement,psam-method plot,psam,ANY-method psam psam-class |
| Class '"pssm"' | $,pssm-method $<-,pssm-method addBlank,pssm,numeric,logical-method as.data.frame,pssm-method coerce() coerce,pssm,matrix-method format,pssm-method matrixReverseComplement,pssm-method plot,pssm,ANY-method pssm pssm-class |
| read pcm from a path | readPCM |
| re-order UPGMA tree | reorderUPGMAtree |
| traceback global | traceBackGlobal |
| traceback local | traceBackLocal |
