7be52d88402cef2f3b68505973862f1b *DESCRIPTION
652376d9407a13949a7e4aaf60a89ac8 *NAMESPACE
32511daa8449bc8c32b708248e20e942 *NEWS.md
4c4737436c143971ad6f742aff246723 *R/binning.R
4eac8dd56dab6dcc13120a40c757d32f *R/monaLisa-package.R
201260f41180f9c52453ba468187d178 *R/motif_enrichment_HOMER.R
2b5001fe9f888e39fcb4d616f78d7d6a *R/motif_enrichment_kmers.R
3cf54f476ec0a2640adce90a35faf0f5 *R/motif_enrichment_monaLisa.R
5fed12e9e66922e36443ee360f697e44 *R/motif_finding.R
e4645aa1d2f5606802ac4a6533bc8f6d *R/pfm_comparison.R
6d43ff561da10316e4f46473b96f6c3b *R/plotBinDiagnostics.R
90ec82571bdc88146904d5ae8acf7dc3 *R/plotting.R
abe604872da595261e49de8f83350055 *R/sample_random_regions.R
ea818964a69b0d94cc3c080d0b4b0487 *R/seqlogo.R
f8eff8c76bc7d86611aaca6e38767518 *R/stability_selection.R
cf1f5ca7c273fe12dccf295dc7ea8723 *R/utils.R
f5271cb75f90db3b0418abfacafec35d *R/utils_enrichment.R
34e30af6554550af1066bb19fbfcc915 *README.md
6c1db45bc4ed3900a7faaba08586701a *build/vignette.rds
ac09bf12137b10a8a59597b835433bc3 *inst/CITATION
4106ffa8a9eb97ec5942de22e968a8cf *inst/doc/monaLisa.R
9930798611a7baf4899853b28955774a *inst/doc/monaLisa.Rmd
d90529c19e81dccfd9000448c752b8b1 *inst/doc/monaLisa.html
21a029560fc4ecd977f5a36d6e27e3a2 *inst/doc/selecting_motifs_with_randLassoStabSel.R
830fdccd37598db6cc0bd7a85e704c1f *inst/doc/selecting_motifs_with_randLassoStabSel.Rmd
40a7919824c1047139e00b4424b050b2 *inst/doc/selecting_motifs_with_randLassoStabSel.html
cdfa02a6f3602d3b845c6c2933886b3e *inst/extdata/LMRsESNPmerged.gr.rds
8442f17323842f86fce25a61678ab28a *inst/extdata/atac_liver_vs_lung.rds
98cf77508f66000eff82aaf29374f412 *inst/extdata/exampleGenome.fa
d7d0749c30353dfc142290ddf62f9884 *inst/extdata/homer_output.txt.gz
b6963ea72edc0fedf31ebba4afaa138b *inst/extdata/results.binned_6mer_enrichment_LMRs.rds
ca8a4b4f11beeb1181cfa11fb009b14c *inst/extdata/results.binned_motif_enrichment_LMRs.rds
fae35211f72620f04f213a7b12828008 *inst/scripts/atac_liver_vs_lung.R
3fab0260b7f3bc8c8b5f99bb1b3721f5 *inst/scripts/binned_motif_enrichment_LMRs.R
459f619704ccd8253ebea164970407d5 *inst/scripts/exampleGenome.R
c0d28675e5bbb40b107974a0af5d91e0 *inst/scripts/generate_plots_readme.R
fe7ab784069739f2a367e27a94a1c33c *inst/scripts/make_sticker.R
a5f3e263dc3b478b0d2163d39275758b *inst/scripts/monaLisa_logo_v1_transparent.png
6ffcf30a2916bd3a5b83af748f13aa6b *man/annoSeqlogo.Rd
2da46835d40474072bc180b1223ae95d *man/bin.Rd
22fe71fac5ad81198d1d7251b3d35aaa *man/calcBinnedKmerEnr.Rd
d658ec3ac6bdc1ca7ee315fb26215494 *man/calcBinnedMotifEnrHomer.Rd
27897fcd34d7f862a55700cda90bd40f *man/calcBinnedMotifEnrR.Rd
d4b793ab3151f67812f1488d7d11e0ab *man/dot-calcKmerEnrichment.Rd
9ff99dd714969fd36146431e6aa7cf30 *man/dot-calcMotifEnrichment.Rd
71d35b37376feb2c8ee7f6e69672808b *man/dot-calculateGCweight.Rd
b4d0e8e9a729e31ab344389b63f92c85 *man/dot-checkDfValidity.Rd
9bdac60d1a061efb16f48be46f83238c *man/dot-checkIfSeqsAreEqualLength.Rd
6a6cf2925f89f3ea8d79f66aa79610bf *man/dot-cons2matrix.Rd
1007f480f9d69eaf7cdd3cd12d704362 *man/dot-defineBackground.Rd
6bf4cd692a16cc830a852d7ad80b1f5b *man/dot-filterSeqs.Rd
be3140bc8d672f29df6d7981b13e82e1 *man/dot-glmnetRandomizedLasso.Rd
f4963865d861852e0e3a66db055810e0 *man/dot-iterativeNormForKmers.Rd
4c94ef61e6a6403bc76ca3ed7d163ee0 *man/dot-normForKmers.Rd
f8c1d9930e6f97566ee7603966c430cc *man/dumpJaspar.Rd
b54e9d657d4d487814a507fa03a3aaf6 *man/figures/monaLisa.pdf
f4d37bb06f001b083d3c5c7d41477c60 *man/figures/monaLisa.png
499d0946dd0543647a395633c6eb1383 *man/figures/monaLisa_binning_small.png
3111bc9b8b9852360a85d3dac3d14e41 *man/figures/monaLisa_binning_small_ggplot.png
2c659600b30ee2381dda19e93c1dcb30 *man/figures/monaLisa_heatmaps_small.png
0a0b8d2807d2c7891c5ac769df4fe24d *man/findHomer.Rd
d0b2517e622836d64462379fb9274db4 *man/findMotifHits-methods.Rd
0debacf296a4b341dd31c03844a36983 *man/getColsByBin.Rd
a24464d7070830e2d2c15a4ff4cae689 *man/getKmerFreq.Rd
5fa1c954cf22963365c53d3fa31fce30 *man/getSetZeroBin.Rd
881157cb388c1ae394b17b846031bd4c *man/homerToPFMatrixList.Rd
412fad3540acbe7fbc2675bca6cc2282 *man/monaLisa-package.Rd
6107310369a465c73a38c86de693803f *man/motifKmerSimilarity.Rd
c8909d468a5aad99d0c365a04d04ed0f *man/motifSimilarity.Rd
bb643fb3b85967abaec73d098573e9a9 *man/parseHomerOutput.Rd
bfd04b3f878648b8f40da2484b0b9ed9 *man/plotBinDensity.Rd
9897a1b1602d3c7e9e962a68b8d2f812 *man/plotBinDiagnostics.Rd
40bd241e8c8ffdbbd5b9f835e64856f5 *man/plotBinHist.Rd
3a3d9d9ede6d17b9b88cae715c615718 *man/plotBinScatter.Rd
3c7b55e1f43ed47977ec9f668c3065da *man/plotMotifHeatmaps.Rd
7e4e8f51ba9c6b902fe5cd0941e0879d *man/plotSelectionProb.Rd
fb71455b2381699118cfc5bcbd763d6c *man/plotStabilityPaths.Rd
cdb2fa729e442bb7f281d43329f72743 *man/prepareHomer.Rd
121f56cb39078feec3bd38aaf3d22a07 *man/randLassoStabSel.Rd
8a710e381becf289222b6c9248706255 *man/sampleRandomRegions.Rd
33d96ea5111fcdc05f593a0c93252c33 *man/seqLogoGrob.Rd
14600bd3a56aa6bebd61256eeccea424 *tests/testthat.R
5cdc0367966c332509ea0ce4e831548d *tests/testthat/test_Homer.R
1ca9cf402f16fbdacb311774f52e00c3 *tests/testthat/test_binned_motif_enrichment.R
236cadf083f022fb0f11d0de1a53f557 *tests/testthat/test_binning.R
abe21accea9000ea534ea7b9b2f9dd3c *tests/testthat/test_kmers.R
4ae3b1bee58af782017d7712d2c812f0 *tests/testthat/test_motif_files.R
4a3d3021d72c5bd2306c2d3724124ce6 *tests/testthat/test_motif_finding.R
f4ae2a83cc490bc4cf50ce7226272bf0 *tests/testthat/test_pfm_comparison.R
058a03ecf9c060bc2868b572c8a190c6 *tests/testthat/test_plotting.R
dbcd1a7b5c54b27b072ab96a8c72320f *tests/testthat/test_sample_random_regions.R
dedc0d7b39c1cd3f85714473e1c8fd18 *tests/testthat/test_seqlogo.R
cafe94a5f66dc5daca65e7b79825e001 *tests/testthat/test_stability_selection.R
ff0a53e368e173b5c7cbea01b0b11ccc *tests/testthat/test_utils.R
c032a7f3e12b6892fa1186f3cb943ac2 *tests/testthat/test_utils_enrichment.R
3c11e0bf01fe236089f9ed05f0297811 *vignettes/monaLisa-refs.bib
9930798611a7baf4899853b28955774a *vignettes/monaLisa.Rmd
830ff5f079bed968eb16a5f51f786438 *vignettes/monaLisa_logo_v1.png
830fdccd37598db6cc0bd7a85e704c1f *vignettes/selecting_motifs_with_randLassoStabSel.Rmd
