0102a4edec2eeeb7b0931bb06c26e0d6 *DESCRIPTION
fd36722cc794efebb6593f2319d53341 *NAMESPACE
ab6ef562fc7cdaf8a728d87a813371d2 *R/BSmooth.R
f52990e883cab50fbceefca1f9be1dc4 *R/BSmooth.fstat.R
2a9881f14bf230afe1914771a75ebd8f *R/BSmooth.tstat.R
aa03724f3378c30edb4a2306b4e1f95b *R/BSseq-class.R
a0e17fb276b2e8ba47057d315eafe66c *R/BSseqStat_class.R
5ab5ae88ada432a9e27b5db8b52b29ae *R/BSseqTstat_class.R
de7654d133d7c157c6bbdee961eb8bd5 *R/BSseq_utils.R
d8c9008ce169e351f470e12a0f9a17ab *R/DelayedArray_utils.R
be03069c93c0755d828063a7e80a9ca0 *R/FWGRanges-class.R
d08ef43d8d3c7c3456f30085189be030 *R/FWIRanges-class.R
fe728d6c12c03ad0f0d4ec0e84599416 *R/Likelihood_functions.R
8365663e9e76e0c1c3a45fb23685793e *R/collapseBSseq.R
26164c14323f7410874e30f4a1a4ab77 *R/combine.R
5cef224e1e962bec12d7f7ddec6bd1c2 *R/dmrFinder.R
bba3e0b63a0d29699ec4693cf5163384 *R/findLoci.R
479640439670c22aaa5766ee62152b58 *R/fisher.R
b86ef3279168fb4eaf90ae171bd3901d *R/getStats.R
c8af97d3a578157d0ce5196cc2bdc2b8 *R/gof_stats.R
9fbb2fa4a9124626e0ff3e480ae40c57 *R/hasGRanges.R
c41be855449062bae4e9aadf7ee877aa *R/hdf5_utils.R
5f8b3cd716ba4e31d27962a68b387482 *R/permutations.R
8988f3a07f8d45874dc150f2c4d46bc8 *R/plotting.R
55d3be93c76ae67b084d1f2dc78a5b3a *R/read.bedMethyl.R
88a4acf4ecfe494420360d3787258e52 *R/read.bismark.R
88540aa5e815e780178326c6f6a09b36 *R/read.modbam2bed.R
a1213400e7027c738e375d4b5e2f6c94 *R/read.modkit.R
7c4abfe808a8bab78b427711224b3871 *R/utils.R
bf85e71acb58f5875f490c2ebe986749 *README.md
89af2c7e69926f518310c44c28f20c06 *build/vignette.rds
ec746595d0d37327ef489856084262b2 *data/BS.chr22.rda
1eb3028e114addfdb22378e4aaf2f0fc *data/datalist
75673927e3869f82667bf8954c9ebca6 *inst/CITATION
9471994b7ac247e00d44d47ed3bbd520 *inst/NEWS.Rd
25befd58f7f7cc7475fe5f6dbaeb83ab *inst/doc/bsseq.R
48a9038af6a1e08a2c79356ca874a42e *inst/doc/bsseq.Rmd
fd33c88251b896fbc91ff5fb6e61fdb1 *inst/doc/bsseq.html
308f4fd1cf7044adae2d1fa4b3b391e5 *inst/doc/bsseq_analysis.R
b53b9896f669115df1547d18c504cf86 *inst/doc/bsseq_analysis.Rmd
a177d02a47dc3c40ea0eeca2f72895f1 *inst/doc/bsseq_analysis.html
7ef001b884f55112e3b3032887a3f81e *inst/extdata/HG002_nanopore_test.bedMethyl.gz
0568a4c5c3568cff8884ff36d9e0795d *inst/extdata/HG002_pacbio_test.bedMethyl.gz
e720da6ab24303994ef3393d878d0d0a *inst/extdata/modbam2bed/ctr1.chr10.chr11.bed.gz
b9b893ffba3cab4b9d44c026f52003c4 *inst/extdata/modbam2bed/ctr2.chr10.chr11.bed.gz
e2d58e241320aea7d7f715dc719f1454 *inst/extdata/modbam2bed/ctr3.chr10.chr11.bed.gz
9fe68dc98602f747df5effb8f2aed803 *inst/extdata/modbam2bed/tret1.chr10.chr11.bed.gz
082df5c7dea37caf2d342ede2098d86c *inst/extdata/modbam2bed/tret2.chr10.chr11.bed.gz
260d2a828add4ff4131e7cea380e649d *inst/extdata/modbam2bed/tret3.chr10.chr11.bed.gz
663d85ed581fa27d7cd368b36f38896d *inst/extdata/modkit/Hypo1.first50Bed.txt
5c30ea0ba02ad252ed80d32d6ab0b6f1 *inst/extdata/modkit/chr21.chr22.HG002.top1000.bed.gz
ba62ab79f68a3d20f3ccc6857fa167a4 *inst/extdata/test_data.cytosineReport.gz
96bb105e35e4b0b0a0ae04d168239996 *inst/extdata/test_data.fastq_bismark.bismark.cov.gz
7e152cd21df27b9b8b2e65111cb30edc *inst/scripts/get_BS.chr22.R
b8e3f3071dcc6cc8fb4b29032d8f1a0f *man/BS.chr22.Rd
62b09d8014b7ec816fa3e50b93dd28a8 *man/BSmooth.Rd
0bf3b064391d6994419acb5f449ff597 *man/BSmooth.fstat.Rd
cdf295355c2d3b2875c24d1bcf14da2a *man/BSmooth.tstat.Rd
dc56200aad5115198865a06be38ec02e *man/BSseq-class.Rd
7489b92d9e851650382c202172ff7db7 *man/BSseq.Rd
3c8d5ee989dbb975a1f50eb9dc910d57 *man/BSseqStat-class.Rd
82f0c86f91921781f70cd10945d86f0e *man/BSseqTstat-class.Rd
9aac846e03040f6c6e8a4f45a5899dd5 *man/FWGRanges-class.Rd
28065955de704e2919a367bfd8aff2df *man/bsseq-deprecated.Rd
5c35f5a7799eed9283b9cadddad2a7ba *man/computeStat.Rd
f2ce6a9996ac9bac8c72d14936e493a4 *man/data.frame2GRanges.Rd
6e5afd8e58d4b5c486e800f567526197 *man/dmrFinder.Rd
ffd012b44a0937e24c2a7321f3ecd526 *man/estimateErrorRate.Rd
d8b777cab5283a9cde4353499695460e *man/findLoci.Rd
e9f0acdb40042d7d3a87f5b5270694ab *man/fisherTests.Rd
d37c224b43efa66f0797232b6b0a9c3f *man/getCoverage.Rd
c44851d7092332d12dece5a645d12f32 *man/getCpGMatrix.Rd
0e4fc0b77da0ecd1fc3963f78e2e1548 *man/getCpGs.Rd
5d7e6b7765eb3bb364dc8a83049dc9a7 *man/getMaxLikelihoodMatrix.Rd
7c0f4fca50aec2eb700e769a56115bd0 *man/getMeth.Rd
9e5abbd087f7010fef0e44cda39eb9f6 *man/getStats.Rd
7cfcc625eeb07949dd956372e62731ea *man/goodnessOfFit.Rd
25a30f814ffcc77ff79add7ccf260939 *man/hasGRanges-class.Rd
3a66ae7c050eeb622ecbd4dc3ec56669 *man/internals.Rd
c8bdaf49935dc23b74397d0bc4a6caa3 *man/plotRegion.Rd
e86b8f8f4a6829b6078e575b7bd91411 *man/read.bedMethyl.Rd
344fba6e83dadea6f4d9400fceb869a4 *man/read.bismark.Rd
0d7ab9f88dbd0603434db7c2d6e9f739 *man/read.modbam2bed.Rd
feddd1b301d0cfb9bc17db95f81f563b *man/read.modkit.Rd
be4248947a83475d0358acaea5ad57e2 *man/smoothSds.Rd
166b36f9a53b6c77abca99457031ee3e *src/BSseq.h
49667f205d72e4172012489da34fe7ea *src/check_M_and_Cov.cpp
7a018270406d66a2025d7b9de58bed62 *src/init.cpp
efce4f034b189dedd1f2d3c117f697ea *src/utils.cpp
82b5c0864013e27abf8df6bdb27b9536 *src/utils.h
b9f9173bc997c1b383a388559dc5739c *tests/testthat.R
1830b04998b0ffdbe21e56cc67170158 *tests/testthat/helper_make_test_data.R
9c44e045aa3b62dc1098f34fd69d8bce *tests/testthat/test_BSmooth.R
909110b7583bc62fcbca984c4f841df1 *tests/testthat/test_BSseq-class.R
aab59047e4dba12e95799850d581b2b0 *tests/testthat/test_GitHub_issues.R
0eb5062ffacef7af1a4fef2c0c4af3ef *tests/testthat/test_HDF5_utils.R
5b19ff82397c2d44c0c479b4d7dc2cfb *tests/testthat/test_base.R
c87bbe2a456edc71eca1f1539e163e9f *tests/testthat/test_check_M_and_Cov.R
e579b59a08c261fd41c6f5bfddeef615 *tests/testthat/test_combine.R
e1b811027fae773e0aeb2425ee4c8b46 *tests/testthat/test_perm.R
f7b96f228134c50b9af5ac2ca0362e42 *tests/testthat/test_read.bedMethyl.R
5fb0fc6b5a2a9f2b545de503473db0fc *tests/testthat/test_read.bismark.R
6544630210ef5da85022ec2a110e397d *tests/testthat/test_read.modbam2bed.R
dfb3036fec9d007f526fcc14b6f8019e *tests/testthat/test_read.modkit.R
e884002b31a037240bea33315f885c04 *tests/testthat/test_utils.R
48a9038af6a1e08a2c79356ca874a42e *vignettes/bsseq.Rmd
83d23c874751123624dc6422db0d42ef *vignettes/bsseq.bib
b53b9896f669115df1547d18c504cf86 *vignettes/bsseq_analysis.Rmd
8a5ad410844b8f334847b40353467211 *vignettes/unsrturl.bst
