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