3fdc4fa42987616c0e069f278bc8323f *DESCRIPTION
a3ee5caf9ebbcae2268019b31a476c21 *NAMESPACE
a8b69ea72653307292a794d55d96d489 *NEWS
eadb7b894527213561ab18869e5247c9 *R/RcppExports.R
d2474316442f4a0760cb3bfcfaeda4d7 *R/adjustMethylC.R
ce64ef296fe47f9e5580fd0742c0da2d *R/backbone.R
3108ba08aa5ab1d2d9770f74bad3f26a *R/batchControl.R
4c02ae01734c48480f621d34051c1f9e *R/bedgraph.R
b8f38138d989025515e4be030b0a6ed6 *R/clusterSamples.R
33602bf13ae1a90ff5b059deb9b492f0 *R/dataSim.R
597a877acd8ea3174740ce6142092025 *R/deprecated_defunct.R
f970edfa6e9567e584456a9d097b57e5 *R/diffMeth.R
a17998928576c94dd807e7c7a4ef2db0 *R/diffMethDSS.R
d1b792f17819378716195aad8768825e *R/document_data.R
69de7129066be7fe6640eaf4225d353d *R/methSeg.R
e048b10fe3bde9120c57e97c584358fc *R/methylDBClasses.R
ece203876d6cab4c93cbdd598af29605 *R/methylDBFunctions.R
7bb95652d67e2b1712595774d5fbab48 *R/methylKit.R
072cc60be0411c2bdc8cdfc56e9582e7 *R/normalizeCoverage.R
d5c7b0a2b426a88446ea1c4337d25c77 *R/onUnload.R
2f1205e34f93fba213fe5ed264970222 *R/percMethylation.R
50910e4f47690d8cafe375508447465c *R/pool.R
3d0e93fe7ba196fa35fcbbfc7f5481c9 *R/processBismarkAln.R
f91ebab31bb0f141dc78ce035a5fa3f8 *R/regionalize.R
ed8f70340d72a6033f1b215c1861520c *R/reorganize.R
56a39a97d67ed3ce559fc9d2becbbd76 *R/tabix.functions.R
cc9c2d324c4eb993a3b199c381e5ea2b *R/updateMethObject.R
11d12e027c24fd31329fc372a93fd89f *README.md
1cd7dff822a8ec5ecc758d0e39906e34 *build/vignette.rds
3098759a5c83a3c45bd159ea9e1bb540 *data/methylKit.RData
10aa55191cbc0781f06a35518262838e *inst/CITATION
3d9925b31c83d2487986260a0441a0d0 *inst/doc/methylKit.R
06faddef74a5d663ca635d8d001851aa *inst/doc/methylKit.Rmd
f5e247d5df0abdfbf554217dd3140f61 *inst/doc/methylKit.html
929f2e9f90436d9bd715782ded751c8d *inst/extdata/bismark_coverage_CpG.bed
f6ca1fe0de1b0a6335001b1ad26d4642 *inst/extdata/bismark_cytosineReport.txt
9f314284ccf1d954a2150d290362033c *inst/extdata/control1.myCpG.txt
c2e87d0e9bf5274c687944cf4fc1b610 *inst/extdata/control2.myCpG.txt
16bc04a2984590a5272c8c9895b6752e *inst/extdata/cpgi.hg18.bed.txt
df0eb6952dc30be700238707958e73bd *inst/extdata/ctrl.bismark_paired_end.sorted.bam
f8b1f2c63f34894df0596b93fd4cc980 *inst/extdata/ctrl.bismark_paired_end.sorted.wh.sam
06ca43dca22648465f17c4f7ab1f6eb1 *inst/extdata/ctrl1.txt.bgz
da59758faa641149dc936ccd1f7d517c *inst/extdata/ctrl2.txt.bgz
e78640ae909e8d97b0fd81b8decfd97a *inst/extdata/generic1.CpG.txt
f8c62c8a9102aee771305f2bc5ba526f *inst/extdata/refseq.hg18.bed.txt
e45fad29dc4f1a3cbaa3a38209b248e0 *inst/extdata/test.bismark_single_end.sorted.bam
069812356c00d6850567db5a6dfc4eb6 *inst/extdata/test.bismark_single_end.sorted.wh.sam
f9a886656e88c673565abc8573ab7541 *inst/extdata/test.fastq_bismark.sorted.min.sam
ed84e619d028dc221cb9b1d2dbe196cb *inst/extdata/test.fastq_bismark.unsorted.min.sam
3fe084e1e464ba316df2a7e20258a87b *inst/extdata/test.fastq_bismark.unsorted_chr.min.sam
320e8a27eb17f29cbd8e5e354265451a *inst/extdata/test1.myCpG.txt
f84407c737c0ac0789cbdc6d15702104 *inst/extdata/test1.txt.bgz
9ec00e7a201362efa9dd460e689e2f53 *inst/extdata/test1_test2_ctrl1_ctrl2.txt.bgz
aa5e23946c668bae0377752e992e3f31 *inst/extdata/test1_test2_ctrl1_ctrl2_diffMeth.txt.bgz
c4992c21174efc8df3129c70f9f65789 *inst/extdata/test2.myCpG.txt
9a9db3f07bfeeac83a815dc02793208a *inst/extdata/test2.txt.bgz
aef8d97d039ef8f54caea88566a96131 *inst/methylKit_logo.png
301b30e38ac4850d4bef6fbe0f33522b *inst/scripts/create.data.R
c1dd0f3af5471242dbb474cd1ee0eaf9 *man/PCASamples-methods.Rd
4fef6189ac569da4d899082c41ad1b9c *man/adjustMethylC.Rd
76a6b6b44f9b0cc5cdd2a9c31f5921f9 *man/assocComp-methods.Rd
d715566ac092b43fcf8faeda5bd88a38 *man/bedgraph-methods.Rd
a8c43bdab0fc6ce25558e817e17d1299 *man/calculateDiffMeth-methods.Rd
b25f52dee282c55d92efea1650212ebf *man/calculateDiffMethDSS-methods.Rd
611e7682f1b623fb0a2b89e7e35c5884 *man/clusterSamples-methods.Rd
bbcebb75e067697e179fe5b66c03a78a *man/dataSim-methods.Rd
9d4bc920c84426bc5bfb40fa6267345d *man/diffMethPerChr-methods.Rd
1df2b5e4296acaf0bd2958e7431583c4 *man/extract-methods.Rd
3972c00ce8355869d9721d78f7f2659d *man/filterByCoverage-methods.Rd
8e4a7c7f2d7c4c9f3175aff39eb06a8f *man/getAssembly-methods.Rd
fc4ce564f30cd7a4badc4b2e9fec4fec *man/getContext-methods.Rd
db519ece1936af670d2aaf022a7413e3 *man/getCorrelation-methods.Rd
23dfa61c41b19ca570ed9125e4863381 *man/getCoverageStats-methods.Rd
7bf4547db0c22ee426022cccbbfa9833 *man/getDBPath-methods.Rd
1c202e6d9da6297ccc417e704b432511 *man/getData-methods.Rd
c9392ca1dd987fae00ec5c71ff3aa11c *man/getMethylDiff-methods.Rd
884551a317769d41687be2a5d17af418 *man/getMethylationStats-methods.Rd
7b3c1a83b81d200b5b80e2f206cd7d47 *man/getSampleID-methods.Rd
09efc05b985dca8962ea9cffdd428c84 *man/getTreatment-methods.Rd
a9d48261a6f349e70a8e761fc5ca2504 *man/joinSegmentNeighbours.Rd
f615a31ecc66cea2c992a9f9c8a97503 *man/makeMethylDB-methods.Rd
2bc44f957158434aff1e875c43935986 *man/methRead-methods.Rd
8af5d8e5deb2d9ba5aba5b5921b57524 *man/methSeg.Rd
8f177c18b39cf352f569cd38352bc31e *man/methSeg2bed.Rd
0ef746b6dd52c0ac6f05497a7e143485 *man/methylBase-class.Rd
3a38ebf03a0bc8af08677dadff72f141 *man/methylBase.obj.Rd
168f55fc17863c5ee787b16c95a4fbd8 *man/methylBaseDB-class.Rd
75efae75e59666427113078178762e49 *man/methylDiff-class.Rd
479e35d3f40aff3ef2f669acbe73d33b *man/methylDiff.obj.Rd
d146bc82f072e2e8ddf42f15bc218c3d *man/methylDiffDB-class.Rd
72f57f82fdfa56fa9e7b90b13364648e *man/methylKit-defunct.Rd
5f0cc2d0c09b2a086da73d9654e94aee *man/methylRaw-class.Rd
724c5d6f9cecb575c91aa5e452b87386 *man/methylRawDB-class.Rd
8df4e5ae3519390f57a6e3e4533fb2a2 *man/methylRawList-class.Rd
5be2c8df539df5f1c92cc7f10f3eafe2 *man/methylRawList.obj.Rd
a3b56687a7e0261260faf4367b4bafa8 *man/methylRawListDB-class.Rd
a5cd51d788bc4dcc020893c9c6bcf1fe *man/normalizeCoverage-methods.Rd
aafe8e31511e87efada1c2a52cbb6511 *man/percMethylation-methods.Rd
04800e77e5c833e85df6196a895c8e7f *man/pool-methods.Rd
117a36ed87259d817c60913d2c36fbe8 *man/processBismarkAln-methods.Rd
e911f97b66f4d078058bf7de35c116e2 *man/readMethylDB-methods.Rd
a7ef824e3599c8b0a13909788214576b *man/reconstruct-methods.Rd
49991e4b262155c4e27f108ab0284062 *man/regionCounts.Rd
406e7ac6fcb7a5c0a19ae404c343ada8 *man/removeComp-methods.Rd
e4ed1b583016a6cbc7d9589c7219df8d *man/reorganize-methods.Rd
ac4ec7d41ffc360a0c051c96e0d13ce6 *man/select-methods.Rd
cfb94a32bfbb51e198c82e05c6aa2b25 *man/selectByOverlap-methods.Rd
462a0587c74abb2ab70ef2011a8cdd1b *man/show-methods.Rd
cf38ce31f0b7d94398b75c2272422be5 *man/tileMethylCounts-methods.Rd
01628767874bdc8c6feb3bc357f83aba *man/unite-methods.Rd
7e4f1f2454d4d3438bef02e24d0a0083 *man/updateMethObject.Rd
c2473c132a96d33201a4dab0d99e0065 *src/Makevars
ce06ab862f239a5e741e78a492d3b6e1 *src/Makevars.win
53b445edcc0e7044f25d567b6a9fcf76 *src/RcppExports.cpp
5c6d8b366288d0409f8d12224de2c675 *src/methCall.cpp
aced91b9a582f15c7528d1f5db9ecf7c *tests/testthat.R
76a0378af13ebec3a2593b0cd93d6b92 *tests/testthat/test-1-methRead.r
aaa4149735ba84dbcdd96af1e0469310 *tests/testthat/test-10-readTabix.r
793eff1e2f7092f3e194c562c4d5a5d0 *tests/testthat/test-11-pool.r
8d2cb664ed0e9c4aee122abe5af38cef *tests/testthat/test-12-selectByOverlap.r
d42bad11e336c85ad9d28ea7278505dc *tests/testthat/test-13-applyTbxByOverlap.r
1992f693526a4d3392940238248ea4f0 *tests/testthat/test-14-methRawListConstructor.r
7aa6c285b96f360230d748ef0664761a *tests/testthat/test-15-adjustMethylC.R
b32b600bad7c800fa79d77c612727275 *tests/testthat/test-16-loadTabix.r
81229b7106f5b8f12c80e3ae98464938 *tests/testthat/test-17-bedgraph.r
6c7f15b6c12c783b4a67a71f7bdf96d8 *tests/testthat/test-18-getMethylationStats.r
af1f08425ea79fedd95cc74e4208f14f *tests/testthat/test-19-getCoverageStats.r
8705a3a225fdda5e4f21206b5fa4acfb *tests/testthat/test-2-unite.r
d44d0ba9f97c486134421748cf06feff *tests/testthat/test-20-normalizeCoverage.r
72c9e91eaed54bd02cd90339caedc5a1 *tests/testthat/test-3-clusterSamples.r
3000650ca75d15c02ca8ef1a9d3c6e6d *tests/testthat/test-4-calculateDiffMeth.r
a19bd967e740e96b598034c579811382 *tests/testthat/test-5-processBismarkAln.r
aee8add5e5431ce9b4139fde22390164 *tests/testthat/test-6-regionCounts.r
5099bbf26ecf2d4f5ebdd06e122e0bf1 *tests/testthat/test-7-dataSim.r
455e50f98af3c9b5152b1469470e5b5d *tests/testthat/test-8-calculateDiffMethDSS.r
8244f0eba05d892cec6b46305fa37392 *tests/testthat/test-8-methSeg.r
b1a77394c9489d10110e32e59c74e856 *tests/testthat/test-999-tidyUp.r
efd743be74b4cea4e8bb3001a265bac7 *tests/testthat/test-batchControl.R
4993559b0c61d7eaf399f3ff146c59cd *tests/testthat/test-diffMethPerChr.R
8fcfff52f016e93ab367a9bc4fc4241d *tests/testthat/test-getMethylDiff.R
b4b6cda9977a98800f77ebb71cd28da3 *tests/testthat/test-methRead_addon.R
8674ddd4404f7816fc3ffd82f19e8ea8 *tests/testthat/test-percMethylation.R
197cdce38eb35a90f32ec640e9463e93 *tests/testthat/test-reorganize.R
47338629469695f9fc483a961ef56f18 *tests/testthat/test-unite_addon.r
80d81165446ea535b4368b5f6375d7a1 *vignettes/Sweavel.sty
adab53441a985793ca871c3f444cecaa *vignettes/Vignette_methylKit.bib
06faddef74a5d663ca635d8d001851aa *vignettes/methylKit.Rmd
