1653e722cb4e18031467cdfaca5055f3 *DESCRIPTION
3759e9720bacf0dab63be2e0ff881483 *INSTALL
d6d8d1be002e04a3aed106fdea6f63e1 *NAMESPACE
7bef3be070acfb4efde026ad363f4d71 *NEWS
03962a36126c11b66347c6a9228f8959 *R/CMEnt-package.R
caa3af1e862c5098b42050089844c822 *R/annotate_dmrs_with_genes.R
c08296e1fbb3cbe387c70027bfd8df27 *R/augment_bsseq.R
3ccf547b3b89c13ab6d05bb0234f9a34 *R/beta_handler.R
c7a8528d42731fbaac63b309089656f4 *R/combine_pvalues.R
8fcbb07e8595c88c85c783e048dd2e55 *R/convert_beta_to_tabix.R
b72d6cf0d4692b4565c2da88ad34053d *R/dmrs_builder.R
8f2bb5d404357979094a801468ed0fb7 *R/dmrs_interaction.R
caca820e5082bc997077ffa7bbe67baf *R/find_dmps_array.R
a816858c64a50956b59e07c260ecca04 *R/find_dmps_bsseq.R
609b739cd1b9b61469841d59858a267f *R/get_dmr_sequences.R
a5ca05cf9cf2652173f5d207b6b0c939 *R/load_example_input_data.R
9aaea1ac2f37d30259040a5253deb739 *R/plot_dmrs.R
b053c4457e279a15daae0ca7d7fb8b1a *R/plot_dmrs_circos.R
0d2db693cfacac2355284e482b226ea4 *R/read_custom_methylation_bed_data.R
1e92fe2aaac15a814c1a459532477d2c *R/reduce_bsseq_around_seeds.R
4c504c8a75a3be6f73acdcb81b2d2415 *R/score_dmrs.R
c31f8499e9f1ef8a40344b1f240734bb *R/shiny_app.R
d97bb9abbbdb282edb76afa0924a29b8 *R/shiny_modules.R
9fe15445c838a92012fbe8a74e59cf8b *R/simulate_dmrs.R
34e9c8a61e3a807452c0293a724c0086 *R/sort_beta_file_by_coordinates.R
66130898d85176bed7b2fd6e2c546f5e *R/sparsify_seeds.R
7df0b78d041f6606df9f398fc2785cf4 *R/utils.R
61aebb8e3255d69c184a87bfc0b75e9f *R/zzz.R
7df7692691a03ca353d5c40b30139830 *README.md
33ac012d37173d7671c8409be2a87d7c *build/vignette.rds
a17f7193923236d868fe8d4bf66e351f *inst/CITATION
33ff54b157d0d7a78d871ebf3d840018 *inst/bin/make_data.R
fac4e4e473859da2da25f9cf56038065 *inst/bin/make_example_outputs.R
c57a66ee0c9974f9f19dafcefcc55968 *inst/doc/cment_example.R
5dd78690e439f47c00996c0ab0f28eae *inst/doc/cment_example.Rmd
6ea30b29f90019281767e04f33e31f84 *inst/doc/cment_example.html
a5156c704946bc41eda0d432f9d461f7 *inst/doc/configuration.R
69cf8724209640cb4bf2d0804f5c6f45 *inst/doc/configuration.Rmd
b00c41a86138b116f880320218b5c47b *inst/doc/configuration.html
825e44be9c2b9fc1e80ab749052d760f *inst/docker/Dockerfile
d44007cf3afd809fd9042ced4e068668 *inst/docker/build_and_push.sh
f6dd09df29a78ee6401be87dc8288c9e *inst/docker/entrypoint.R
3d998a2873d25108e6cf8444fa164ab8 *inst/docker/install_dependencies.R
0ac2ce379154e1758e52c6864ed3a882 *inst/docker/run_cment.R
79a0effea4e56d33a26b3e2276ad156d *inst/extdata/README
618e1c2e46d12206689269e341f3f9ba *inst/extdata/example_outputChr5And11.dmrs.tsv.gz
889704f8d2db17093d7e51424a6ec669 *inst/extdata/example_outputChr5And11.meta.rds
a4e56b7589b3f465fd06da09883c003f *inst/extdata/example_outputChr5And11.rds
6e9cbe303fd57747469df8c943feec6d *inst/extdata/example_pheno.rds
8262d6cdaada5352ab8200a87e914b46 *inst/extdata/supportedOrganisms.csv
fb3d69665b4d066e0fb470b547ef6c37 *inst/shiny/CMEntViewer/app.R
4c00fccfb7f97becdd30a9e64133108d *inst/shiny/CMEntViewer/www/custom.css
f7d50515b8dd6c380adb1e8f3345e9d4 *inst/shiny/CMEntViewer/www/logo.png
2f93c323641b2d31787b4867ad6faff6 *man/BetaHandler.Rd
afa7bf055183b845023589a76fdb9256 *man/CMEnt-package.Rd
c884af87ca8b58550221252e22d2012e *man/annotateDMRsWithGenes.Rd
fcaf8c757dc684eb08e6e1789324e456 *man/augmentBSSeq.Rd
ab8de8e46659fd62945ed8bfa99b2e61 *man/buildDMRs.Rd
72a5924a0b1c8cba758ea3b988d0a8a4 *man/combinePvalues.Rd
fe49583a854f83e2b5d7469d501648b9 *man/computeDMRsInteraction.Rd
d9936eb490dac03880c94ede19267894 *man/convertBetaToTabix.Rd
97016b357f1e562395104e0b156bd01a *man/extractDMRMotifs.Rd
56bccd7f8eb0252056e971c829fae77c *man/figures/logo.png
3fd32784934f6132b0f71dd13b06013e *man/findDMPsArray.Rd
831998a9dcda164a4a832090faffe229 *man/findDMPsBSSeq.Rd
7366ee13d2d0ea2f2e865d91fc1e650f *man/getBetaHandler.Rd
66a519cfed07d57cafad94ce81a59b4f *man/getDMRSequences.Rd
f8aff8e506b957ab1bdb6eb42de52c87 *man/getSortedGenomicLocs.Rd
d1f4a46746c31598e066ed906d105e33 *man/launchCMEntViewer.Rd
f72d15fb384a060d333d9962105d0e82 *man/loadExampleInputData.Rd
b77b128b7a1cc8608692760fa7b6dc74 *man/orderByLoc.Rd
963ec4d803642b7c9b758597b2b2713e *man/plotAutoDMRsCircos.Rd
c2f87f701d603edff18d13c0352d081f *man/plotDMR.Rd
591e968b6ef0eaa5f13e4600f00bfb7c *man/plotDMRBlockFormation.Rd
442e73e465bcb6ebabf29c1c7dff312d *man/plotDMRs.Rd
0f1a74ce6f970526754fc91d7d2fac6b *man/plotDMRsCircos.Rd
0ca84e47e454aa9af9d297954ac499d0 *man/plotDMRsManhattan.Rd
2b127ed64316035f714859ffd564844d *man/readCustomMethylationBedData.Rd
c86fea528d6c8789fb2f8d00f97eeca0 *man/reduceBSseqAroundSeeds.Rd
c59fd9b63ec71764f970973f9d87665e *man/scoreDMRs.Rd
04f3b6dbe7c4d10af0723b22c20986b1 *man/simulateDMRs.Rd
e37075393236e6ed0bd7637877c97b23 *man/sortBetaFileByCoordinates.Rd
c1bb7cb7a26c05b386ce893ec09c655f *man/sparsifySeeds.Rd
2cfb444d9a0613898dd0e8d1aa5a3d0b *tests/testthat.R
aa8cd4d906c393ace235d174d6a38aa0 *tests/testthat/helper-dependencies.R
983d6e419c8889c53b68e88a2751cb64 *tests/testthat/helper-synthetic-fixtures.R
fd06c79ba139e456d7bd7e255d43c093 *tests/testthat/test-annotateDMRsWithGenes.R
d8e4fc3801f90c6df03be5ae8cb443ec *tests/testthat/test-augmentBSSeq.R
8d0bd9528217c1e3a3cdfb4b81597972 *tests/testthat/test-beta-file-subsetting.R
e58b94ccfe52f9a6db9f1b4f6e4f9ccd *tests/testthat/test-betaHandlerBSseq.R
03f03cff734ee2a800fbd976c6d5b592 *tests/testthat/test-betaHandlerColNames.R
f961a7c81b1864f65695537580f944a8 *tests/testthat/test-biocfilecache-paths.R
ec3a944e2369130fbf766a6393eab3f3 *tests/testthat/test-buildDMRs.R
24a1d571aa99dd71cf267fb4cf3b065c *tests/testthat/test-buildDMRsDifferentInputs.R
507374dcb737340517df30e2d15c1478 *tests/testthat/test-buildDMRsGenomeDefaults.R
2e7e0db7cd91db598c765a374f208765 *tests/testthat/test-buildDMRsInputOrdering.R
ec7a80af38e1e9fdff880a774482551b *tests/testthat/test-buildDMRsStage2.R
181a7fd8ad174b954a2883355f867171 *tests/testthat/test-buildDMRsStage2Params.R
13e3da59e071ebc1a1bde40909263854 *tests/testthat/test-buildDMRsWithBedFileInput.R
c16eefd8c773a79f870af96b15bd9c0f *tests/testthat/test-buildDMRsWithDifferentPvalComputation.R
4dd453311a5019f919ebb989c9bab1a2 *tests/testthat/test-buildDMRsWithWeakEntanglement.R
19247168b7d2d83e34804ba4f0f27f38 *tests/testthat/test-cli.R
ad6a186754d96df504d0fee5c0ce5753 *tests/testthat/test-combinePvalues.R
62a60383f3bafb223802a5c3f5355c26 *tests/testthat/test-computeDMRsInteraction.R
8eab82ba2d03d82f1a3e3e71ace4ebe5 *tests/testthat/test-container-dependencies.R
e2ab433d75f373a8d705a80bf92d0175 *tests/testthat/test-dependency-checks.R
17bfb49fa54643c882053d8e689fe8ac *tests/testthat/test-findDMPsArray.R
da91cb2a53e1333ae68dd2dcab65ace8 *tests/testthat/test-findDMPsBSSeq.R
d8d64362d7a66ca3aa4f6d59e1692125 *tests/testthat/test-getDMRSequences.R
fed645183d20f89b7f2fdabc71c15996 *tests/testthat/test-getSortedGenomicLocs.R
fb17b998322c90a1ec0fea73f61e32be *tests/testthat/test-hs1-support.R
7281d9d902914e40538fde78bf0f21ae *tests/testthat/test-loadExampleInputData.R
c7d63d67963c998a3899e387f99f3bf7 *tests/testthat/test-output_serialization.R
9e8bd5b7b2e1737467401e1dd7a27a2a *tests/testthat/test-plotDMRs.R
b6cb634be6672adeee6dda338adc8c4f *tests/testthat/test-plotDMRsCircos.R
53baece940cec997f41b3e0dfc408129 *tests/testthat/test-plotDMRsManhattan.R
dd7e1670797a4602fe5531d2904b3dc6 *tests/testthat/test-reduceBSseqAroundSeeds.R
7e4b24e15b76974b4dadde87e4f3f286 *tests/testthat/test-registry-hdf5.R
6db0d08c5dd4b8618fc1a82fb0830f92 *tests/testthat/test-scoreDMRs.R
4281316fc81c9079efdeed2fd2b7337c *tests/testthat/test-shiny_viewer.R
b820594bd8500c13340547be9cbf326d *tests/testthat/test-shiny_viewer_helpers.R
009ea9155c6a21a148d8b3ce1c003d4d *tests/testthat/test-simulateDMRs.R
9523a0f12eac54d8a1ff12fedf353397 *tests/testthat/test-utils.R
5dd78690e439f47c00996c0ab0f28eae *vignettes/cment_example.Rmd
69cf8724209640cb4bf2d0804f5c6f45 *vignettes/configuration.Rmd
