Man pages for jianhong/motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
| AAmotifAlignment | align AA motifs |
| browseMotifs | browse motifs |
| browseMotifs-shiny | Shiny bindings for browseMotifs |
| calF | calculate frequence |
| calI | calculate I' |
| clusterMotifs | cluster motifs |
| colorset | retrieve color setting for logo |
| compare2profiles | compare two profiles |
| compareProfiles | comapre w pcm |
| DNAmotifAlignment | align DNA motifs |
| DNAmotifToRNAmotif | convert DNA motif into RNA motif |
| dpGlobal | Global alignment version |
| dpLocal | Dynamic programming function, local version |
| geom_motif | geom_motif |
| GeomMotif | GeomMotif object |
| getALLRscoreFromCounts | calculate ALLR from counts |
| getDistance | Calculate distances between two profiles |
| getRankedUniqueMotifs | get the unique motif in each category grouped by distance |
| getScore | Calculate pair_wise position score |
| highlightCol | add alpha transparency value to a color |
| importMatrix | import motifs from local files |
| marker-class | Class 'marker' |
| matalign | Matrix Aligner |
| mergeMotifs | merge multiple motifs |
| motifCircos | plot sequence logo stacks with a radial phylogenic tree and... |
| motifCloud | plot a DNA sequence logo cloud |
| motifGrob | Motif Grob |
| motifHclust | Hierarchical Clustering motifs |
| motifPiles | plot sequence logo stacks with a linear phylogenic tree and... |
| motifSig-class | Class '"motifSig"' |
| motifSignature | get signatures from motifs |
| motifStack | plot a DNA sequence logo stack |
| motifStack-package | Plot stacked logos for single or multiple DNA, RNA and amino... |
| ouNode-class | Class 'ouNode' |
| pcm-class | Class '"pcm"' |
| pfm2pwm | convert pfm object to PWM |
| pfm-class | Class '"pfm"' |
| plotAffinityLogo | plot affinity logo |
| plotMotifLogo | plot sequence logo |
| plotMotifLogoA | plot sequence logo without plot.new |
| plotMotifLogoStack | plot sequence logos stack |
| plotMotifLogoStackWithTree | plot sequence logos stack with hierarchical cluster tree |
| plotMotifOverMotif | plot motif over another motif |
| plotMotifStackWithPhylog | plot sequence logo stacks with a ape4-style phylogenic tree |
| plotMotifStackWithRadialPhylog | plot sequence logo stacks with a radial phylogenic tree |
| plotXaxis | plot x-axis |
| plotYaxis | plot y-axis |
| psam-class | Class '"psam"' |
| pssm-class | Class '"pssm"' |
| readPCM | read pcm from a path |
| reorderUPGMAtree | re-order UPGMA tree |
| traceBackGlobal | traceback global |
| traceBackLocal | traceback local |
