76900b21aae92f6655d0c0136c44923d *DESCRIPTION
1b4479ef380a54868428e658e9b915bc *NAMESPACE
65938cc8b21b2fa28a9c474b26280ada *R/DMRcaller.R
2b29b823931c28b79b80eb3323de85c3 *R/ONTdata.R
1cc64f082ef388f6014b8c3a5292cff9 *R/Replicates.R
86acf08758184589592ee5f39029a6cb *R/computeCoMethylatedPostions.R
725dcc85042031ba2959bf8269b3f83e *R/computeCoMethylatedRegions.R
ce4e91e502dc79386836f571e17eb5c0 *R/computeDMRs.R
e94638053e59e84d3b4331941c715c52 *R/computePMDs.R
a090e44c507cccfa08a929360ba4a306 *R/computeVMDs.R
9334181b093e64451c91422ade4ac5e4 *R/coverage.R
42f19969b0b50984423944a25ac48bda *R/extractGC.R
52965950f92d580ba9f1313b4859f3e5 *R/filterVMRsONT.R
d1b7b4a83a924ca82e3aed8ee91e2815 *R/generalFunctions.R
2ea92e159f961dcdc4e88cc57a058dfa *R/loadData.R
54f6d808e7ccd23adf571ddc707c5ccc *R/localProfile.R
63ee8dc16ed343085cb8c6eca9275b00 *R/movingAverage.R
0c8c43705a1fe5334fb5747ffa5a6646 *R/profile.R
a7f13d1d1fa31c6bc407af00f60550d4 *R/regions.R
5f197e534492cd2e7a2c4e6a0ed27331 *R/spatialCorrelation.R
bcf1e555f19a4a0c77f77f3e082338ba *R/statisticalTests.R
fca84adb6965e126425e1007c136c2ce *build/vignette.rds
1c8211047fa13376845e7f3956155713 *data/DMRsNoiseFilterCG.RData
8f0fad11ada832a94df73e5769a01aa2 *data/GEs.RData
4c27b4446f35aaa364288cc7af787f1e *data/GEs_hg38.RData
f992e3fd671817f45653e10c0d4c770d *data/PMDsBinsCG.RData
43c8112cee381de1b33cc398e7270749 *data/PMDsNoiseFilterCG.RData
d88b1272159019fa3efa975c819891fc *data/datalist
df3d2b4a2be049d24bb51f05d1cc079e *data/methylationDataList.RData
620e384af0cb0f2b4b95b8e07948f5d9 *data/ontSampleGRangesList.RData
1090b1f47148d53ce38db449be12418c *data/ont_gr_GM18870_chr1_PMD_bins_1k.RData
6596c072138e658feb36e7b9e9c00a5f *data/ont_gr_GM18870_chr1_sorted_bins_1k.RData
b2db81d597dc8db4312d8d54fa388a55 *data/syntheticDataReplicates.RData
5b81fb4d1878a998a73845e942fc22e0 *inst/CITATION
1bb2b20b6ebe4ef442609df52e16225a *inst/NEWS
980b3f0c69c1cc6dde1fa9901befd1ac *inst/doc/DMRcaller.R
4a0c2528a481aeb420f90ef800cf2d28 *inst/doc/DMRcaller.Rmd
937b3899258a1a5419d1bc89768dff02 *inst/doc/DMRcaller.html
ae51776ed063a8a5c00295c5136e040e *inst/extdata/scanBamChr1Random5.bam
6b03b55fb4d60a5afa8835a37152349d *inst/extdata/scanBamChr1Random5.bam.bai
89b64592650a37a6304bf7c227848d5a *inst/unitTests/test_DMRcaller.R
828c3e3e5177a9e325eeefaec5e44d9c *man/DMRcaller.Rd
3b130ef6ceaccd7c2856cfd863291106 *man/DMRsNoiseFilterCG.Rd
caeab8c5580fdc5acae6603a420872ac *man/GEs.Rd
ead8b69d53aab9bd2c31a926b3fad81e *man/GEs_hg38.Rd
a0d376d53704a293d4faf1b02d735d2b *man/PMDsBinsCG.Rd
9287c049a75a8d711d5a43b6d7920db2 *man/PMDsNoiseFilterCG.Rd
f69bf7f6d6050376dd0b7bb71de86961 *man/analyseReadsInsideRegionsForCondition.Rd
58087d89560f4a6569f658c1cfd072f3 *man/analyseReadsInsideRegionsForConditionPMD.Rd
c141ded0cdf0c45a008329058c7759f0 *man/computeCoMethylatedPositions.Rd
e8e66eb7dba9f2e3547e176dd61bb57a *man/computeCoMethylatedRegions.Rd
65260d27be95c8f3a25b22185b9e2680 *man/computeDMRs.Rd
10c4a15a67710cdd2cea03f626e42a26 *man/computeDMRsReplicates.Rd
c012632ed8abe2a2fff53a6432459659 *man/computeMethylationDataCoverage.Rd
b200aa82757c27ae09bb3d624c891fb7 *man/computeMethylationDataSpatialCorrelation.Rd
1decd5b14d820926a1afecb140e2e9ae *man/computeMethylationProfile.Rd
956a66ce534464b1b7f28c128192a567 *man/computeOverlapProfile.Rd
91a5ba005501393a6425404201442006 *man/computePMDs.Rd
cf50fb0ad16ff5938828c64ba1fcf12b *man/computeVMDs.Rd
8904b7d49372ea4dd7c03a0aa544c96e *man/extractGC.Rd
1268b87c90b0749541dbd42caf13e5f9 *man/filterDMRs.Rd
5f3c20bc99b2bed6040bff85e30a5cad *man/filterPMDs.Rd
d0841f6ac5e18488d5069e01801d21ba *man/filterVMDs.Rd
5327e777828075a4fbbeec66f82a3555 *man/filterVMRsONT.Rd
0078bf5dda6ffc17bd2e548436d26999 *man/getWholeChromosomes.Rd
50ddd265de1293d0d693453419e6c596 *man/joinReplicates.Rd
69727213c7eda2f3e9d69f32d4e06f01 *man/mergeDMRsIteratively.Rd
ac712d162b8d223a33e8c7706e6eb557 *man/mergePMDsIteratively.Rd
e3f5caa367e9eb61ec895395820b4059 *man/methylationDataList.Rd
0229007426919ed669a76c2ef4473fba *man/ontSampleGRangesList.Rd
82d6638e1a080a58d3c0e3c8aa1a8f0f *man/ont_gr_GM18870_chr1_PMD_bins_1k.Rd
8f87c00056cd3e839990e3b82cf6099d *man/ont_gr_GM18870_chr1_sorted_bins_1k.Rd
551519757d1298d7ec8260f43be1c942 *man/plotLocalMethylationProfile.Rd
a84f4d4006b08b76b0f7fd30a33f1b1d *man/plotMethylationDataCoverage.Rd
22a2b74ea7e1555423ac1f0c5a86bfc6 *man/plotMethylationDataSpatialCorrelation.Rd
a4a8367d98d6c5832aed8addb3937306 *man/plotMethylationProfile.Rd
5a282093fc958d1b342ca1e697a38a76 *man/plotMethylationProfileFromData.Rd
a795bdd0d30e55bb539196bdf09c5f15 *man/plotOverlapProfile.Rd
c9072bceee8f0f85107b8644c127a108 *man/poolMethylationDatasets.Rd
80a78b2c8669b067fb5115007700a3dc *man/poolTwoMethylationDatasets.Rd
abfa0d8e17eebf6df0d7f6089bad7197 *man/readBismark.Rd
c609fe282beb0e4f01bce1d6cbc0a7eb *man/readBismarkPool.Rd
e7784bd3e06d5704c54d03a8c1f32c58 *man/readONTbam.Rd
c6da46a2a26daded35943ec3630c9423 *man/saveBismark.Rd
c5231ae9d6aaaf6c2bd40eb2f1ce1de2 *man/scanBamChr1Random5.Rd
30e57458dca591a6dc70b297db1eb1b8 *man/selectCytosine.Rd
1e65f7d52d67c2843047a46fa152b07a *man/syntheticDataReplicates.Rd
eb7f44f29f77104f9f67b7737ca5947d *tests/runTests.R
4a0c2528a481aeb420f90ef800cf2d28 *vignettes/DMRcaller.Rmd
c4c91d3e4c30b44b4edd3ca3a11a2a3b *vignettes/DMRcaller.bib
0a7068e2a54ccffc75dbf8d0c4b133b8 *vignettes/apa.csl
