Man pages for fmicompbio/monaLisa
Binned Motif Enrichment Analysis and Visualization
| annoSeqlogo | Sequence logo annotation |
| bin | Bin elements of 'x'. |
| calcBinnedKmerEnr | Calculate k-mer enrichment in bins of sequences. |
| calcBinnedMotifEnrHomer | Prepare and run HOMER motif enrichment analysis. |
| calcBinnedMotifEnrR | Binned Motif Enrichment Analysis with 'monaLisa' |
| dot-calcKmerEnrichment | Calculate k-mer enrichment |
| dot-calcMotifEnrichment | Calculate motif enrichment |
| dot-calculateGCweight | Get background sequence weights for GC bins |
| dot-checkDfValidity | Check if seqinfo DataFrame is valid |
| dot-checkIfSeqsAreEqualLength | Check if elements of 'x' are have equal lengths |
| dot-cons2matrix | Create matrix from consensus sequence |
| dot-defineBackground | Define background sequence set for a single motif enrichment... |
| dot-filterSeqs | Filter Sequences |
| dot-glmnetRandomizedLasso | Randomized Lasso |
| dot-iterativeNormForKmers | Adjust for k-mer composition (multiple iterations) |
| dot-normForKmers | Adjust for k-mer composition (single iteration) |
| dumpJaspar | Dump Jaspar motifs into a HOMER motif file. |
| findHomer | Find HOMER script file. |
| findMotifHits-methods | Find motif matches in sequences. |
| getColsByBin | Get colors by bin. |
| getKmerFreq | Calculate observed and expected k-mer frequencies |
| getSetZeroBin | Get and set the zero bin manually |
| homerToPFMatrixList | Read a HOMER motif file and create a PFMatrixList |
| monaLisa-package | monaLisa - MOtif aNAlysis with Lisa. |
| motifKmerSimilarity | Calculate similarities between motifs and k-mers. |
| motifSimilarity | Calculate similarities between pairs of motifs. |
| parseHomerOutput | load output from HOMER findMotifsGenome.pl into R |
| plotBinDensity | Density plot of binned elements. |
| plotBinDiagnostics | Plot diagnostics of binned sequences |
| plotBinHist | Histogram of binned elements. |
| plotBinScatter | Scatter plot (xy-plot) of binned elements. |
| plotMotifHeatmaps | Heatmap of motif enrichments. |
| plotSelectionProb | Plot selection probabilities of predictors |
| plotStabilityPaths | Plot Stability Paths |
| prepareHomer | Prepare input files for HOMER motif enrichment analysis. |
| randLassoStabSel | Randomized Lasso Stability Selection |
| sampleRandomRegions | Sample random regions of fixed length. |
| seqLogoGrob | Create a simple sequence logo grob. |
