9da4df59b650cccebf18a8a4036b85b8 *DESCRIPTION
2721f09c2a1a5f62ee9524c10c2dead7 *LICENSE
3f9e467fb259f23492c497d206e18331 *NAMESPACE
154c59af3a31d571e9e4a18c94d54c43 *NEWS.md
f4c2138655d0044d616b48e3ec66b0d0 *R/RcppExports.R
13b5227c01284b4dc2962846b16fafaf *R/addOffsets.R
4acd030893362e90d41261821e6adb75 *R/base-EM.R
21638b835bca9fd3b4641eefe760937e *R/base-checkers.R
402d534f56e7aa74b8da770f2bd80e57 *R/base-core.R
be3a9c0b9b0f3c36ebe7daf202ddc1cb *R/base-loglikelihood.R
5035c21d487a857ce4b0f1fab6b4d3a1 *R/base-optim.R
91ee4836eae416c0c203d7fe03b849de *R/base-utils.R
407cfa1e29ba863d0b1464f13a990a24 *R/base-wrappers.R
3c1ad548ac5c1c31a9df45b7df291083 *R/base-writers.R
8d96c81e7e14d26ba56baea262ddefe2 *R/callPaterns.R
a566d8d29d0928f747d29f62c93654af *R/callPeaks.R
59752b730c174a6e03a1ac6d23a1e65b *R/cleanCounts.R
68aea4fd0d0291125b3971e3931206ba *R/controlEM.R
d976158b755b9453f19160055e671dda *R/data-helas3.R
a0ccb1dd203e6638d8183866aa474117 *R/epigraHMM-package.R
7af375164778e5cc4fc8ceb1fcc8874b *R/epigraHMM.R
057c18e7b8dc72961716d67d321a9e86 *R/epigraHMMDataSetFromBam.R
0d3a91e491cdcabb1d225d9f37f971cc *R/epigraHMMDataSetFromMatrix.R
f86a48a63955d6eb2dc238252fc580fc *R/estimateTransitionProb.R
d225e5a9b94e10427b4c8fa269b2d5ac *R/info.R
bed3ace4c24ba899ce6691072027c81f *R/initializer.R
3be76c0cf3afac248fca1b52d43a2348 *R/normalizeCounts.R
b4e2af31cd97dce97b56d2b555b8a54c *R/plotCounts.R
90950dd0f01c25c7e11b433f3708f092 *R/plotPatterns.R
32ddcc38d53b9bd5a11d4127b42281e4 *R/segmentGenome.R
b8a7af1dd0c58a426a8cadd004a09237 *R/utils-data-table.R
7151dbe5c8df85d3688dbddd7dcd5b4a *R/utils-pipe.R
6d993244a472b9141f4cd6527beabb5e *README.Rmd
336a2b87186a4101c7350ac56a9c316a *README.md
b685a12d16e8e1130197e23839c56174 *build/vignette.rds
42330f5e2fdf4e2078a378ab870daa90 *data/helas3.rda
109de2bf84a4813362f466f6b98b9648 *inst/doc/epigraHMM.R
b16eab68cf0b726cd5b9e15f5cf5b603 *inst/doc/epigraHMM.Rmd
ebcd820d6a885842b3e4b1cb6945f769 *inst/doc/epigraHMM.html
9d3fb9c8fb7b9bbff01c0ec1c06ca4a1 *man/addOffsets.Rd
fcf12f45ffb6d4f891ac2031c1e313c2 *man/callPatterns.Rd
1210ae8a8dae6f4e511c4746152a0fc2 *man/callPeaks.Rd
c9159a018ab9b784e31c4672b8d804a5 *man/cleanCounts.Rd
8082b63bdc0eaa9b7058eeabf40f8a15 *man/controlEM.Rd
b6f76f660ddfcf2137913f614847718e *man/epigraHMM.Rd
d9becb7b48dbead551ce79cfbc8bcc44 *man/epigraHMMDataSetFromBam.Rd
11c1aa782c230ed4418cbda49b85c39a *man/epigraHMMDataSetFromMatrix.Rd
399ea5bb6458adf0e06d901693790504 *man/estimateTransitionProb.Rd
57c61de947c98e82a71a8c00f6f37534 *man/expStep.Rd
b3151444cd3af8451dc518130e4d3345 *man/helas3.Rd
6f584441b5466c1d1c5b2d19b92f1fce *man/info.Rd
5a43ce2dc7becd434ba08e9bc38230cc *man/initializer.Rd
100f4b44aacd8f8b9b8d432588053221 *man/maxStepProb.Rd
ed2a9276749dfb1998584ca96a7785df *man/normalizeCounts.Rd
c95a2ec0ba4bfafc97035a708684b876 *man/plotCounts.Rd
8cb82b7697179a3e3ecf3e269d0bb91e *man/plotPatterns.Rd
21769d78823bafd398195cefa8c2cc5c *man/segmentGenome.Rd
9b46e92fcc882a44e253ce54b3ff812b *man/simulateMarkovChain.Rd
6f6ff5d5e540ca04194f7f6e7a648956 *src/Makevars
6f6ff5d5e540ca04194f7f6e7a648956 *src/Makevars.win
0e4ca31a68b16f85b262822a9e8a3639 *src/RcppExports.cpp
7430f48bb514a80da777a9bd64a63042 *src/aggregate.cpp
e897574286dd010eaa179a35d4f12072 *src/aggregate.h
4b583a3ddb9e25ba53a123b78f476083 *src/computeBIC.cpp
64c0165862ab22522fcae06d22e3ef6e *src/computeQFunction.cpp
98032187c8551f6224f6d00d0367f942 *src/computeViterbiSequence.cpp
af3cbb1ebe92b921d1e914b11a2c3c65 *src/consensusRejectionControlled.cpp
5bdb7c105ffd28ded74ea1102429222a *src/differentialRejectionControlled.cpp
160d4dba93e5707545acd9307697cf27 *src/expStep.cpp
548398c5d193b3f54be23db3a50d8641 *src/getMarginalProbability.cpp
38000a3540e0ca5f55d0de1a0b87438f *src/innerMaxStepProb.cpp
6a9249c049312bafebb68c447ea6f1c1 *src/maxStepProb.cpp
b12845e977aec82d7ed87e108a5efbfb *src/rbinomVectorized.cpp
6bd163ada48c06a00af203450a690a1c *src/rbinomVectorized.h
0a10c3e66f64655ba6a7a9da950e0916 *src/reweight.cpp
c59664e988bb707dba9bddfbc1e0f209 *src/reweight.h
cdfa422bed7a15dfbdce4e69fbf11905 *src/simulateMarkovChain.cpp
94eeb447b6d99965d74acaa7f45a273a *tests/testthat.R
a5ab80b675082cf7c841c5108bf852b4 *tests/testthat/test-addOffsets.R
4e4296b96a69835205b2c6678597942b *tests/testthat/test-base.R
a66715f87a331ba2a52f2c0f4d404580 *tests/testthat/test-callPeaks.R
21f969c464b545bab06be5d0c1bc4e76 *tests/testthat/test-cleanCounts.R
85ac61e82b2b70f1b5e261dbfd5b3d0d *tests/testthat/test-controlEM.R
eb2b2109f7fdb735f21b8b62bb3fc369 *tests/testthat/test-epigraHMM.R
bd8aabbfdf35bf4f4ca1f83edd59b4d8 *tests/testthat/test-epigraHMMDataSetFromBam.R
c69e73f90f3c1cdb2fb5d9c29e7ca481 *tests/testthat/test-epigraHMMDataSetFromMatrix.R
9c174deaf168ccbaa2db232b55055738 *tests/testthat/test-initializer.R
cbbcb8eef4a17c986c6d2f5865aa064f *tests/testthat/test-normalizeCounts.R
b7c45f7007796ea1b5efc8ad85d1bd0d *tests/testthat/test-plotCounts.R
39f43e04f362bc54489157ea2d1ca6df *tests/testthat/test-plotPatterns.R
8b5d7acd7a476b8550aa21743110bfbf *vignettes/bibliography.bib
b16eab68cf0b726cd5b9e15f5cf5b603 *vignettes/epigraHMM.Rmd
