e97d94bb46d2ffa99bdd1d3afef9e3c8 *DESCRIPTION
e364d3a653d4d925a8d4677f4fd3fe45 *NAMESPACE
f37bfccc159d6be49c500e73baa31125 *NEWS.md
c2fd0642a4a466303455b29b275f2c27 *R/Baseline.R
169fb4acc0e443470dab716e60fea3d0 *R/Core.R
c1ea211ad71f2eb8df5fee0b7052bd42 *R/DistToNearest.R
499c3e8d2f4bc7efb2b8dcd6b6ff3922 *R/MutationDefinitions.R
aa461c39aeffdfa1b3b43c421c303e10 *R/MutationProfiling.R
35824350a3c17012f4cbf17e0a3cfe24 *R/RegionDefinitions.R
ca8396f1cea72d2044d3b6e7fa538dd4 *R/Shazam.R
1312673bb338647bcbcef10e470b8627 *R/Shmulate.R
71c65cdf15d10b5c18dacd8348cb8cfe *R/TargetingModels.R
1d821cc64741432266cc41d5995e2393 *R/sysdata.rda
2b732279471f311c9cca7493c5de57d1 *README.md
fad9e3aee84b45d31784d974861cba20 *build/vignette.rds
a6d8e4bb225163a04252376b3b2fe3b5 *data/CHARGE_MUTATIONS.rda
7e859498fb0f1bb1b751c2f868c2f64d *data/HH_S1F.rda
705021bff606e05cbf8b1b1ac8baa98e *data/HH_S5F.rda
ae1d42042a9029a2d146c7a39f9e6ab5 *data/HKL_S1F.rda
27129af2f0ed571f92d0e342a98ab5e0 *data/HKL_S5F.rda
27d7bdb4a59fb7e157790b5df263a24e *data/HYDROPATHY_MUTATIONS.rda
7fa7745ee395660b9b46e3cdc2abafdf *data/IMGT_V.rda
c999307b3aab9a120b9a84c74c6a192f *data/IMGT_V_BY_REGIONS.rda
5633195e71ba4c44b944fb77150cac72 *data/MK_RS1NF.rda
017563e018bbe5251fbfc59118da7685 *data/MK_RS5NF.rda
c9c22320df42880769b793bea91ded36 *data/POLARITY_MUTATIONS.rda
448dfac6d9d746b89eb8856e2462eee6 *data/U5N.rda
ae6ab7434ee43157d8e8b2921f223c85 *data/VOLUME_MUTATIONS.rda
f3b50c606aaca388ab4155ea3428f454 *inst/CITATION
339c8faa3b6f3efedef5dbb5016fc7a3 *inst/doc/Baseline-Vignette.R
1c51f2e53fb386188445cf9adcae877c *inst/doc/Baseline-Vignette.Rmd
68f5b656b8b6d622d464d53751263134 *inst/doc/Baseline-Vignette.pdf
8b7c02df2a8df927928da6a0be4adeaf *inst/doc/DistToNearest-Vignette.R
81338d2a15d7826ce29d853060f90602 *inst/doc/DistToNearest-Vignette.Rmd
4778d3394ccb35a02e202a9a8dc0ab7b *inst/doc/DistToNearest-Vignette.pdf
b6b832e21bd1732c584bd5150bd14ac7 *inst/doc/Mutation-Vignette.R
503be66ef35bfed0f8fa4276e7cb5497 *inst/doc/Mutation-Vignette.Rmd
be75c8c0562740e23623a10e9613ecc4 *inst/doc/Mutation-Vignette.pdf
7a94e409727fcb9cb0de4b8404244a4c *inst/doc/Targeting-Vignette.R
1785012971a135beb456f26bb9d1c144 *inst/doc/Targeting-Vignette.Rmd
7e5f6bb1097733d6c5b556a8ffb1e06d *inst/doc/Targeting-Vignette.pdf
bdf3c40f1ad2693ec1a4ae1a380ec962 *inst/markr/build.R
3168b8357b34479aa188c7d7dfb016fb *man/Baseline-class.Rd
194f0b0b407e448970f26b92ac858f62 *man/DensityThreshold-class.Rd
b22695efd032eccaf58fa278433383b6 *man/GmmThreshold-class.Rd
98f6d6aeaadf58389960f586c02b3882 *man/HH_S1F.Rd
d7cad825b7d37ca0c856b785bf892b5f *man/HH_S5F.Rd
a138d04fc9b94bda4d43f77c0c34f64f *man/HKL_S1F.Rd
9ea9a7a7240150a9f983975ce17348f5 *man/HKL_S5F.Rd
0c77fdfd892635844b9d637d5c58e309 *man/IMGT_SCHEMES.Rd
d1cf9c4e6bcd13ac03bee4022cca7dda *man/MK_RS1NF.Rd
5a0b0b68f073d362ed921d7ce2b6d302 *man/MK_RS5NF.Rd
b52702a03ac31b18ced1ff1a8236b367 *man/MUTATION_SCHEMES.Rd
13787752e7a8c6d36e4580366cb8be82 *man/MutationDefinition-class.Rd
37bdc51c60fd3366a48546265720756e *man/RegionDefinition-class.Rd
aa59dd1f421239362dff00f8af2069a5 *man/TargetingModel-class.Rd
9bbb541c44b6ca3ee17d2ae8e1b03d31 *man/U5N.Rd
8c6816de404b3f44da5f1a7fc118695c *man/calcBaseline.Rd
f7fe5e20697f92665982b293ec2ed96c *man/calcExpectedMutations.Rd
8cbc105d4fa29cb4ce77e3afafb8cdfa *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
0e531760f7839c686640b0319d814aaa *man/clearConsole.Rd
61d49889989a0be9fdc15df8f5da6404 *man/collapseClones.Rd
b1389cc1a3d3cab1d7a424f1e0093566 *man/createBaseline.Rd
3d329f4039b26e162c06ceaa668a7599 *man/createMutabilityMatrix.Rd
291078043a96c53414245a7e245510d4 *man/createMutationDefinition.Rd
e3eefd932cca9d511015287438a68be1 *man/createRegionDefinition.Rd
618dd94638eb5e346eb9971693067c00 *man/createSubstitutionMatrix.Rd
55e9db243c04b84f7119d5320ce01148 *man/createTargetingMatrix.Rd
6fa3236ec6548ccab5fa2a074fba9833 *man/createTargetingModel.Rd
179bffd1e62f3e4c0385c82fb90f0eba *man/distToNearest.Rd
c48aebad10772e16266ab6bf42e5a525 *man/editBaseline.Rd
1b41dcea61bdc2a1bccd5e1b90184d68 *man/expectedMutations.Rd
9e56bc899a938d5c0000c274e20c37ee *man/extendMutabilityMatrix.Rd
92510a9afa61258fb8ec6fce367678eb *man/extendSubstitutionMatrix.Rd
c62e8be4f45c2d86d21fe47351a5fdfa *man/findThreshold.Rd
5588c1aa700ae660c350c277f981cfe0 *man/getBaselineStats.Rd
34d212a2ad15aa008786ac14d9a446c5 *man/getPlatform.Rd
80b4bf39e1a72c5c3f47d2af3a1ae237 *man/getnproc.Rd
7123fa3c7872e7d329886e4aa6408672 *man/groupBaseline.Rd
a64599327530e7dd2e26c79dc2bf27ae *man/makeAverage1merMut.Rd
d3ad96cd8466448271e018d0774ebb44 *man/makeAverage1merSub.Rd
a421abd5d1b8546f15e2926a3d3d601d *man/makeDegenerate5merMut.Rd
f1e35fb60180aa5226b1ca07fab136c2 *man/makeDegenerate5merSub.Rd
5c137ef63008e49040fb72e0d5a928ae *man/minNumMutationsTune.Rd
ad2ab10e1ca9d6fdfd3f46d4919f55a9 *man/minNumSeqMutationsTune.Rd
b38f294086065482d99d42cc7076c894 *man/observedMutations.Rd
01c91386554fce80d027d67a8f040935 *man/plotBaselineDensity.Rd
3f8499c966f78f9492e18f7e0d5b9eab *man/plotBaselineSummary.Rd
0c5072593ae66cb82a1aa541ed737370 *man/plotDensityThreshold.Rd
f4abd43ca254a704af0cefd518c14276 *man/plotGmmThreshold.Rd
1b77a8f7e030450365ed5c35f93cfcad *man/plotMutability.Rd
b857609a88f4a8d6b394e1f9810ca19d *man/plotTune.Rd
d172e5a22c5fd8fa46376e9092dd847d *man/shazam.Rd
189d5dddef9436868b8a0c5df4c6a650 *man/shmulateSeq.Rd
b56295d58b780bce387b3aec56504986 *man/shmulateTree.Rd
4dcdb117521ce07eb3a4df5684842517 *man/slideWindowDb.Rd
f0aa8aae1bb4f145b69190e2d11bb9fb *man/slideWindowSeq.Rd
767e9d40a932571948ffc26936abc443 *man/slideWindowTune.Rd
61830750932b532c0cfbbe0f55a05573 *man/slideWindowTunePlot.Rd
719322e1cb9943b976f2e1d0e030b2a2 *man/summarizeBaseline.Rd
168b021d274d220d3226b24f9e6088df *man/testBaseline.Rd
fa559348ea1c62b9ff781eb8f4232071 *man/writeTargetingDistance.Rd
1c51f2e53fb386188445cf9adcae877c *vignettes/Baseline-Vignette.Rmd
81338d2a15d7826ce29d853060f90602 *vignettes/DistToNearest-Vignette.Rmd
503be66ef35bfed0f8fa4276e7cb5497 *vignettes/Mutation-Vignette.Rmd
1785012971a135beb456f26bb9d1c144 *vignettes/Targeting-Vignette.Rmd
