1970d0dc3b44cdf4b371bfe54e67eafc *DESCRIPTION
fc136619efee2929659a442152e2c569 *NAMESPACE
ab6ef562fc7cdaf8a728d87a813371d2 *R/BSmooth.R
f52990e883cab50fbceefca1f9be1dc4 *R/BSmooth.fstat.R
a95dc16e7585300882d14bf050c87f85 *R/BSmooth.tstat.R
7da03bbe712439b42bffc507a6517d35 *R/BSseq-class.R
a0e17fb276b2e8ba47057d315eafe66c *R/BSseqStat_class.R
5ab5ae88ada432a9e27b5db8b52b29ae *R/BSseqTstat_class.R
99e4e117aa9e4c6c091ebee4e36f57c5 *R/BSseq_utils.R
03e02dcdb51a1d77e859b8110d389c65 *R/DelayedArray_utils.R
be03069c93c0755d828063a7e80a9ca0 *R/FWGRanges-class.R
d17c4b73a33f0ad3481f7386197f1e37 *R/FWIRanges-class.R
760e6d0453577fa1075ab27dea05e019 *R/Likelihood_functions.R
20e9a8c3b8095cbe37aae62f3c5ec055 *R/MethylCounts.R
93fe92e99dd41487f27e26419dd1a0f5 *R/check_bedMethyl.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
5704013f13f91826a58a186a23b03c2a *R/read.bedMethyl.R
88a4acf4ecfe494420360d3787258e52 *R/read.bismark.R
8ddeafbaa07f22d81009cae7df3fba3d *R/read.modbam2bed.R
fccb91838be271fa43bea270a723887c *R/read.modkit.R
254259d5d6615cdcfc65cbbd2c6a0432 *R/utils.R
93aeafbc69d6d38ae984f1d19ca09e09 *README.md
ea59b5d60f811d37dbbd70de76393179 *build/vignette.rds
ec746595d0d37327ef489856084262b2 *data/BS.chr22.rda
1eb3028e114addfdb22378e4aaf2f0fc *data/datalist
75673927e3869f82667bf8954c9ebca6 *inst/CITATION
783b8be6ce9820a0199cdae817a49749 *inst/NEWS.Rd
68b298e8a84cf403c073faafc3a268c8 *inst/doc/Longread_guide.R
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0eece163be3660daed68e9469e61d3a1 *inst/extdata/longread/silversides/all_cpgs/AR3.bedmethyl.gz
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ba54da921acd3da31ca78315301223ab *inst/extdata/longread/silversides/all_cpgs/RR2.bedmethyl.gz
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b9b893ffba3cab4b9d44c026f52003c4 *inst/extdata/modbam2bed/ctr2.chr10.chr11.bed.gz
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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
d1a447338ac6c3e177ed51fa54fdd6f4 *man/BSmooth.tstat.Rd
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9aac846e03040f6c6e8a4f45a5899dd5 *man/FWGRanges-class.Rd
269acd882f54dc1d1dd44d4650e3ec0f *man/MethylCounts-class.Rd
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6e5afd8e58d4b5c486e800f567526197 *man/dmrFinder.Rd
7cbd86522471e404b854230eb0574adf *man/estimateErrorRate.Rd
d8b777cab5283a9cde4353499695460e *man/findLoci.Rd
e9f0acdb40042d7d3a87f5b5270694ab *man/fisherTests.Rd
d37c224b43efa66f0797232b6b0a9c3f *man/getCoverage.Rd
7dd3d94da53595bc27ff0d1e5fa4c426 *man/getCpGMatrix.Rd
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7c0f4fca50aec2eb700e769a56115bd0 *man/getMeth.Rd
9e5abbd087f7010fef0e44cda39eb9f6 *man/getStats.Rd
7cfcc625eeb07949dd956372e62731ea *man/goodnessOfFit.Rd
25a30f814ffcc77ff79add7ccf260939 *man/hasGRanges-class.Rd
3a66ae7c050eeb622ecbd4dc3ec56669 *man/internals.Rd
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344fba6e83dadea6f4d9400fceb869a4 *man/read.bismark.Rd
be4248947a83475d0358acaea5ad57e2 *man/smoothSds.Rd
166b36f9a53b6c77abca99457031ee3e *src/BSseq.h
49667f205d72e4172012489da34fe7ea *src/check_M_and_Cov.cpp
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b9f9173bc997c1b383a388559dc5739c *tests/testthat.R
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c6e266bd474257562cc6ed195889f213 *tests/testthat/test_BSmooth.R
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aab59047e4dba12e95799850d581b2b0 *tests/testthat/test_GitHub_issues.R
0eb5062ffacef7af1a4fef2c0c4af3ef *tests/testthat/test_HDF5_utils.R
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e579b59a08c261fd41c6f5bfddeef615 *tests/testthat/test_combine.R
e1b811027fae773e0aeb2425ee4c8b46 *tests/testthat/test_perm.R
cbcbef4f0773c31850fa2a9eb2828790 *tests/testthat/test_read.bedMethyl.R
5fb0fc6b5a2a9f2b545de503473db0fc *tests/testthat/test_read.bismark.R
e884002b31a037240bea33315f885c04 *tests/testthat/test_utils.R
0a08322cf5cfb8ecd05b7a03720e4714 *vignettes/Longread_guide.Rmd
42868f5297b2638b195d325f97fd1d12 *vignettes/bsseq.Rmd
e9a4a7750a7ee00c4f20e95fa353d554 *vignettes/bsseq.bib
b53b9896f669115df1547d18c504cf86 *vignettes/bsseq_analysis.Rmd
8a5ad410844b8f334847b40353467211 *vignettes/unsrturl.bst
