633ccf2c59fe20c4756e14be357b2a26 *DESCRIPTION
e07eb8489228002638d7eecfd204eea6 *NAMESPACE
3946ce53d86fcab2ec4116f0a0f449bd *NEWS
f5a725b9a74895fc4e6fb7f0a8d3db79 *R/AllClasses.R
4908586afa02c2f7dba9fd64c6868b39 *R/AllGenerics.R
79cd3af93099ceb7aa4b793100d90aa7 *R/adjustBoundary.R
ad8d1b5abebe3e47424e34977538b132 *R/base_adapGridMosaicsZ0_IO.R
ca16c213623b546106acde8008b20af9 *R/base_adapGridMosaicsZ0_OS.R
16ea5b339d644fc6b67b0775f2208d48 *R/base_adapGridMosaicsZ0_TS.R
8d67081a96883b2aef1e6de63590d79e *R/base_annotateHMM.R
f0c2b1ffc7b826dff854b2c1aa4b04a0 *R/base_annotatePeak.R
91e279036de58b4ee2471bd67594d665 *R/base_calcModelBIC.R
54d29c46d9913ae5a75757d5e1041e31 *R/base_calcPN.R
d67c8ef8cf2f4949d1e2e5e0ddb2d526 *R/base_calcYbdAll.R
b4a457bebf8e5eb8c41e0fef241a32e0 *R/base_computeStat.R
59d5c4b1a08b17952fb2707dc44266a7 *R/base_constructExtRead.R
8e870b05718bcef20dcecc57df481e41 *R/base_convolution_1S_cpp.R
4e9b9cbda44b34cfcca1e0cda08a534f *R/base_convolution_2S_cpp.R
3763f1bdaf86daa7eaf16317a2b2a7e6 *R/base_cpp_call.R
ffc92f40ba8f3d43c2964d40df27a66d *R/base_export.R
bd4ea145d4135eea8fc9289c7524a995 *R/base_extractPostProb.R
90a4a1a9cb7d20d6dcd2b6867e9f2fd7 *R/base_fitHMM.R
78a7eb069afc131df81b3f9ba83f994c *R/base_getParamZ0.R
94205a48e2a45f8762c8c7ef8c7e6037 *R/base_getPi0.R
987f0436a413cb33cf22aca42ff01737 *R/base_loadReadData.R
fa37426b3e5188d29046325db9fc25c4 *R/base_logLik.R
0e87cbf1366daafdd321cf4dc776f4a1 *R/base_margDist_1S.R
2cd419838725187a341f9c9d28eea6fb *R/base_margDist_2S.R
cb0b9608d0a41e401d7c99ea29755797 *R/base_mosaicsZ0.R
3dd0c1672c254fe9379652ef24ea3917 *R/base_mosaicsZ1_1S.R
3077e8f2659f2edea78934931f01f786 *R/base_mosaicsZ1_2S.R
3e7d32b0524137a91ed6b221138310a4 *R/base_peakCall.R
5787c966470e9931270a99284925b9cf *R/base_plotGOF.R
3336e43a5d729e88e4d8c0ab3251fced *R/base_plotGOFHMM.R
6b199b45500ad8ae5cf9cb6b4bf79ec1 *R/base_reportSummary.R
1921e2c3c0567c8c007f90b5b6609770 *R/base_rlmFit_IO.R
f5a52582a64067e97dd22060b342cd5f *R/base_rlmFit_OS.R
2c154134679aab33bd5b08cd0d050a9d *R/base_rlmFit_TS.R
280e9822a60af31f28a9c09884761576 *R/base_trimExtend.R
ef1559dfe3c75f6226231e74dce3024a *R/constructBins.R
80840f5a3cc269780c079905d27598cc *R/extractReads.R
68be79bbf3ecbee7d530769d41ba7b81 *R/filterPeak.R
aaf07d39a7a7813c7a068fff263d2c3a *R/findSummit.R
76864abf38e59722da27970c9bf9066f *R/generateWig.R
ed65df3fda4d2641c058fd6e31853a72 *R/methods_BinData.R
01a47ff362674554ba633019ca874291 *R/methods_MosaicsFit.R
58fdd4016439be892f605ecadded1eba *R/methods_MosaicsHMM.R
1cba7dc1df0d9fb9dcbd5393f0d7bab6 *R/methods_MosaicsPeak.R
03264672fd99f46f7b7231852c9e338f *R/mosaicsFit.R
dc2753f9b3ea0a152265aa8f7e96d1f9 *R/mosaicsFitHMM.R
775b1aa8d47da640cfa80895e1662074 *R/mosaicsPeak.R
afdacb3f7a61328acf2d31e7a6a155f5 *R/mosaicsPeakHMM.R
da189a4f3c35d38aa62c50b6ac4f0085 *R/mosaicsRunAll.R
8a74ef9691fe19d3d5db1860df99f772 *R/readBins.R
26d09bcb2f179c9c62c60fd4e95f0f98 *build/vignette.rds
00cf0d31dd9d13869e62e19396a46cd6 *inst/Perl/convert_csem_format.pl
6e1ee3548119d658a678af3b98d726f2 *inst/Perl/csem_wrapper.pl
cca9566ef6ab0b7413a8d556b209fb68 *inst/Perl/extract_coord_PET.pl
5ab3b53dcd6bf81a066d5ba958b2d47c *inst/Perl/extract_coord_SET.pl
ef5a748e1dc1a5757d3bac5b9931bb70 *inst/Perl/process_readfiles_PET.pl
1128ec8d0da6c6463e8e4152675e0c1e *inst/Perl/process_readfiles_SET.pl
28e60bc97e0b4346d151614dfb3db2dd *inst/Perl/readfile2wig_PET.pl
9537931980fc8561444291680bc9075a *inst/Perl/readfile2wig_SET.pl
bc9e5696303c8239f1b02c6fd161bc40 *inst/doc/mosaics-example.R
ed2a386019872833c39b0d74e780ab86 *inst/doc/mosaics-example.Rnw
2e7cfa79a66f564b96ac0fd78c52ac81 *inst/doc/mosaics-example.pdf
37ec91247875a1a9cd107bbf3ac53b6d *man/BinData-class.Rd
b4fe54bc9f6db5f4a9c2eee165471d4f *man/MosaicsFit-class.Rd
4da192eb7fd15e3b44dc170a82bc60cf *man/MosaicsFitEst-class.Rd
d113a87334fc646af021380c9263f772 *man/MosaicsFitParam-class.Rd
55480fa4d24ec65ba9a84d3596cb0452 *man/MosaicsHMM-class.Rd
805716935ce7fd874e92c8823ec0590f *man/MosaicsPeak-class.Rd
afb51b00d1bdfbef1543794e9e1e8c5a *man/MosaicsPeakParam-class.Rd
24fd08375c2af04871d3bbf97de90fb9 *man/TagData-class.Rd
e1613c59fccc049a0df661d8ab7c9d55 *man/adjustBoundary.Rd
d72036c39b93b8d0528be4b1ed4333a5 *man/constructBins.Rd
106174be1ec30456e16b1298afe2bfc9 *man/estimates.Rd
1b6ea01b4e2a8a77424c4bac71b5703c *man/export.Rd
1f2300c2da2cb5d1277fa7ee084491c8 *man/extractReads.Rd
bb8c95a6f1f8b00411c4900ff5eeb7b2 *man/findSummit.Rd
6bb179d85943ddf1d83592485d20540b *man/fllterPeak.Rd
a09094be1e8a51eb9509fec200b483c9 *man/generateWig.Rd
93c85c26932969be49c177805fce5d50 *man/mosaics-internal.Rd
c59d3a7f15eb638975eea55cc93a5e15 *man/mosaics-package.Rd
e734368d5a333f0fb63f36f89b6b7544 *man/mosaicsFit.Rd
f540270741e25692983016800bc85288 *man/mosaicsFitHMM.Rd
0307e1f5a4519af3f075ce6123fa36ff *man/mosaicsPeak.Rd
297818fc4aee0aad3c9700e26600d1ed *man/mosaicsPeakHMM.Rd
7094f8b26b101fb8973286488ded1614 *man/mosaicsRunAll.Rd
393e25d72fea5ce9a01c5d3eb1d0765c *man/readBins.Rd
f896f637df014c2b192e82668b49e3f1 *src/convolution_1S.cpp
9f77233cdf12f9787c43013bf7db64aa *src/convolution_2S.cpp
0b79488922dfcecdcd12152c50808312 *src/emHMM.cpp
09a332960faa122f479f2053dbcb9f2b *src/stack.cpp
fe7184780b1076b2a98fac5bb586e6bd *src/updatePiMat.cpp
29bcaec7dd78c6d9430f1c7c0cb612bc *src/viterbi.cpp
5a0b9b318f63aac9593ebf4048a7a799 *vignettes/Figure4a.pdf
64c528ff77b351429de20621d4f8a11c *vignettes/Figure4b.pdf
f514570c2ebb9a570f5c39e662122cb8 *vignettes/Figure5a.pdf
26d751796cf1fe75afe1e4512a0bd1f4 *vignettes/Figure5b.pdf
a6632dfde843eff7421d7c5f98d47519 *vignettes/Figure5c.pdf
0e8ce14c09bacf7f7e5389ab3223bd01 *vignettes/Figure5d.pdf
5dc22da4eb39a7b3095b3001071a0304 *vignettes/GOF_matchLow.pdf
145cdfccd1e279034641251893a0b0f0 *vignettes/GOF_rMOM.pdf
6cd69b85d06005cea4e14bda42068d91 *vignettes/igv.pdf
ed2a386019872833c39b0d74e780ab86 *vignettes/mosaics-example.Rnw
