79de84f37bd2d7d91b44faf7c1e1eab0 *DESCRIPTION
36b6dabd83ac74dd5bf19e10834b97fb *NAMESPACE
ab6ef562fc7cdaf8a728d87a813371d2 *R/BSmooth.R
f52990e883cab50fbceefca1f9be1dc4 *R/BSmooth.fstat.R
2a9881f14bf230afe1914771a75ebd8f *R/BSmooth.tstat.R
95c9187c7dcace9b763f29bb138e2537 *R/BSseq-class.R
a0e17fb276b2e8ba47057d315eafe66c *R/BSseqStat_class.R
5ab5ae88ada432a9e27b5db8b52b29ae *R/BSseqTstat_class.R
de7654d133d7c157c6bbdee961eb8bd5 *R/BSseq_utils.R
d8c9008ce169e351f470e12a0f9a17ab *R/DelayedArray_utils.R
011e0e64da6906892b45748fb454b366 *R/FWGRanges-class.R
d08ef43d8d3c7c3456f30085189be030 *R/FWIRanges-class.R
003da449cddbc76d25e0f99f0d937280 *R/collapseBSseq.R
33979c395211c1fc54ca1fec9c88137a *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
a96345589f491cd10ca102b13be8d525 *R/read.bismark.R
ee22d7211bd25bb82ca0aae0ad1a5b9c *R/read.modbam2bed.R
b0c4e1597b0e5f51461324271fadb4d3 *R/read.modkit.R
7c4abfe808a8bab78b427711224b3871 *R/utils.R
bf85e71acb58f5875f490c2ebe986749 *README.md
ffc92b7d118f543f5f8e24ce32086731 *build/vignette.rds
ec746595d0d37327ef489856084262b2 *data/BS.chr22.rda
1eb3028e114addfdb22378e4aaf2f0fc *data/datalist
75673927e3869f82667bf8954c9ebca6 *inst/CITATION
945b4d566f2e0c046cf22e121d56f042 *inst/NEWS.Rd
697b09153a3685f602c2a97e77076f6a *inst/doc/bsseq.R
ec426eb389d60536e10e973fa5ef9c1e *inst/doc/bsseq.Rmd
40bf39b4bf507ed0d631b692891c5346 *inst/doc/bsseq.html
16bf08acfc524043aab43b6c86f1272a *inst/doc/bsseq_analysis.R
b53b9896f669115df1547d18c504cf86 *inst/doc/bsseq_analysis.Rmd
c1024a51cf4bc9ae7050a465c86ae70a *inst/doc/bsseq_analysis.html
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
c9e15232f79b8e85a0fed3e719c73b6e *man/BSmooth.Rd
0bf3b064391d6994419acb5f449ff597 *man/BSmooth.fstat.Rd
cdf295355c2d3b2875c24d1bcf14da2a *man/BSmooth.tstat.Rd
26a47207864fe201cfefb7f008ab0069 *man/BSseq-class.Rd
bd072b9f54af4196072d96f8a9d9c601 *man/BSseq.Rd
e3277e42a100ec93e415cf29237f29d5 *man/BSseqStat-class.Rd
651ec1d4d4956978987749594112ed79 *man/BSseqTstat-class.Rd
9aac846e03040f6c6e8a4f45a5899dd5 *man/FWGRanges-class.Rd
5c35f5a7799eed9283b9cadddad2a7ba *man/computeStat.Rd
f2ce6a9996ac9bac8c72d14936e493a4 *man/data.frame2GRanges.Rd
6e5afd8e58d4b5c486e800f567526197 *man/dmrFinder.Rd
24865e13bcb5b10af7d0e6dfdd863bd2 *man/findLoci.Rd
e9f0acdb40042d7d3a87f5b5270694ab *man/fisherTests.Rd
6bde3f69e88161892eae9af76a731196 *man/getCoverage.Rd
780d85e95952f57d07ac0f8303d789df *man/getMeth.Rd
9e5abbd087f7010fef0e44cda39eb9f6 *man/getStats.Rd
7cfcc625eeb07949dd956372e62731ea *man/goodnessOfFit.Rd
25a30f814ffcc77ff79add7ccf260939 *man/hasGRanges-class.Rd
3a66ae7c050eeb622ecbd4dc3ec56669 *man/internals.Rd
c8bdaf49935dc23b74397d0bc4a6caa3 *man/plotRegion.Rd
25c49936136e0ea617bbba1cead633ae *man/read.bismark.Rd
da0869738ac13a3ca58e299e20d10856 *man/read.modbam2bed.Rd
4a98ea9282f2d869e866c5abb6b43b2d *man/read.modkit.Rd
be4248947a83475d0358acaea5ad57e2 *man/smoothSds.Rd
79bf72e578bcc74a3a6110115b506bcd *src/BSseq.h
5662aa80f67bff897921df105ae0b2f1 *src/check_M_and_Cov.cpp
97480cdbb825cb2142dab39511348dfe *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
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
ec426eb389d60536e10e973fa5ef9c1e *vignettes/bsseq.Rmd
236f2938c35e80e98e8da5cab570b9e0 *vignettes/bsseq.bib
b53b9896f669115df1547d18c504cf86 *vignettes/bsseq_analysis.Rmd
8a5ad410844b8f334847b40353467211 *vignettes/unsrturl.bst
