├── .Rbuildignore ├── .github └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── binning.R ├── monaLisa-package.R ├── motif_enrichment_HOMER.R ├── motif_enrichment_kmers.R ├── motif_enrichment_monaLisa.R ├── motif_finding.R ├── pfm_comparison.R ├── plotBinDiagnostics.R ├── plotting.R ├── sample_random_regions.R ├── seqlogo.R ├── stability_selection.R ├── utils.R └── utils_enrichment.R ├── README.md ├── _pkgdown.yml ├── inst ├── CITATION ├── extdata │ ├── LMRsESNPmerged.gr.rds │ ├── atac_liver_vs_lung.rds │ ├── exampleGenome.fa │ ├── homer_output.txt.gz │ ├── results.binned_6mer_enrichment_LMRs.rds │ └── results.binned_motif_enrichment_LMRs.rds └── scripts │ ├── atac_liver_vs_lung.R │ ├── binned_motif_enrichment_LMRs.R │ ├── exampleGenome.R │ ├── generate_plots_readme.R │ ├── make_sticker.R │ └── monaLisa_logo_v1_transparent.png ├── man ├── annoSeqlogo.Rd ├── bin.Rd ├── calcBinnedKmerEnr.Rd ├── calcBinnedMotifEnrHomer.Rd ├── calcBinnedMotifEnrR.Rd ├── dot-calcKmerEnrichment.Rd ├── dot-calcMotifEnrichment.Rd ├── dot-calculateGCweight.Rd ├── dot-checkDfValidity.Rd ├── dot-checkIfSeqsAreEqualLength.Rd ├── dot-cons2matrix.Rd ├── dot-defineBackground.Rd ├── dot-filterSeqs.Rd ├── dot-glmnetRandomizedLasso.Rd ├── dot-iterativeNormForKmers.Rd ├── dot-normForKmers.Rd ├── dumpJaspar.Rd ├── figures │ ├── monaLisa.pdf │ ├── monaLisa.png │ ├── monaLisa_binning_small.png │ ├── monaLisa_binning_small_ggplot.png │ └── monaLisa_heatmaps_small.png ├── findHomer.Rd ├── findMotifHits-methods.Rd ├── getColsByBin.Rd ├── getKmerFreq.Rd ├── getSetZeroBin.Rd ├── homerToPFMatrixList.Rd ├── monaLisa-package.Rd ├── motifKmerSimilarity.Rd ├── motifSimilarity.Rd ├── parseHomerOutput.Rd ├── plotBinDensity.Rd ├── plotBinDiagnostics.Rd ├── plotBinHist.Rd ├── plotBinScatter.Rd ├── plotMotifHeatmaps.Rd ├── plotSelectionProb.Rd ├── plotStabilityPaths.Rd ├── prepareHomer.Rd ├── randLassoStabSel.Rd ├── sampleRandomRegions.Rd └── seqLogoGrob.Rd ├── tests ├── testthat.R └── testthat │ ├── test_Homer.R │ ├── test_binned_motif_enrichment.R │ ├── test_binning.R │ ├── test_kmers.R │ ├── test_motif_files.R │ ├── test_motif_finding.R │ ├── test_pfm_comparison.R │ ├── test_plotting.R │ ├── test_sample_random_regions.R │ ├── test_seqlogo.R │ ├── test_stability_selection.R │ ├── test_utils.R │ └── test_utils_enrichment.R └── vignettes ├── .gitignore ├── monaLisa-refs.bib ├── monaLisa.Rmd ├── monaLisa_logo_v1.png └── selecting_motifs_with_randLassoStabSel.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fmicompbio/monaLisa/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yaml: -------------------------------------------------------------------------------- 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