cf3ec268da89fcbd6b50d4672b3afd6e *DESCRIPTION
51f62d18623310ac69b9850390eb7f0c *NAMESPACE
66ecff258c7f18c91872a43657371208 *NEWS.md
e86e5699d9b9195bb31b387da7cedced *R/Baseline.R
3e346a2116e587aaa015b7596bb31ee8 *R/Core.R
2b4f3105f1c3628f2e71840bf1d77f30 *R/DistToNearest.R
14ba6753a414a6c7608e8eb9740fe35c *R/MutationDefinitions.R
4db83b3dbff419bf9de3ffe27e4572fd *R/MutationProfiling.R
35824350a3c17012f4cbf17e0a3cfe24 *R/RegionDefinitions.R
d98daeb436d3eeb21fdf49c084a982d0 *R/Shazam.R
6b59b26dd3225759c381539b4b74077b *R/Shmulate.R
23df52190986d4b38e6fdd737a47462d *R/TargetingModels.R
a38c85416a33e60fe3eadcedd8390a0f *R/sysdata.rda
2b732279471f311c9cca7493c5de57d1 *README.md
fad9e3aee84b45d31784d974861cba20 *build/vignette.rds
e7e3fb96f13ebe5ff7f30a204c44f112 *data/CHARGE_MUTATIONS.rda
7e859498fb0f1bb1b751c2f868c2f64d *data/HH_S1F.rda
705021bff606e05cbf8b1b1ac8baa98e *data/HH_S5F.rda
ae1d42042a9029a2d146c7a39f9e6ab5 *data/HKL_S1F.rda
27129af2f0ed571f92d0e342a98ab5e0 *data/HKL_S5F.rda
7d621c815a2cf4be20eaa0354d77501a *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
5a4160145b4bba0f76066726274c8cf6 *data/POLARITY_MUTATIONS.rda
448dfac6d9d746b89eb8856e2462eee6 *data/U5N.rda
b5164066cf2fd04b883d9342f9f37093 *data/VOLUME_MUTATIONS.rda
f3b50c606aaca388ab4155ea3428f454 *inst/CITATION
b5e345df4e9a41612ce739e4031ad6eb *inst/doc/Baseline-Vignette.R
2218ce33605d0f7ea3e484af66d23b72 *inst/doc/Baseline-Vignette.Rmd
aeb7ada4e294ff84b8bd7a1886cab625 *inst/doc/Baseline-Vignette.pdf
8b03f9aceaa708d20dc8649d9d23991a *inst/doc/DistToNearest-Vignette.R
637ad37b1c2042ca1a54f7edf3016892 *inst/doc/DistToNearest-Vignette.Rmd
acaea714d327f1657ad32abafbfdcab8 *inst/doc/DistToNearest-Vignette.pdf
2c0e7ac002e5fe56010d603225dfa6e2 *inst/doc/Mutation-Vignette.R
5701dc3e14b9afe4c57997afcf67f975 *inst/doc/Mutation-Vignette.Rmd
a5a822e9eea44c93f587345c6d7d8b1a *inst/doc/Mutation-Vignette.pdf
7a94e409727fcb9cb0de4b8404244a4c *inst/doc/Targeting-Vignette.R
1785012971a135beb456f26bb9d1c144 *inst/doc/Targeting-Vignette.Rmd
0e1ceb965f5787f617d027d81c58edaf *inst/doc/Targeting-Vignette.pdf
bdf3c40f1ad2693ec1a4ae1a380ec962 *inst/markr/build.R
3168b8357b34479aa188c7d7dfb016fb *man/Baseline-class.Rd
194f0b0b407e448970f26b92ac858f62 *man/DensityThreshold-class.Rd
5ee85fc17e35509d99b837268db83c4a *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
9845b5734b3c177b0706f20c6f870586 *man/calcBaseline.Rd
c44906bfd418b47762ddb01b13aa329a *man/calcExpectedMutations.Rd
c72613bef01e0456deb615951120ee5d *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
0e531760f7839c686640b0319d814aaa *man/clearConsole.Rd
c4cfb21f6c8ad4d73749429d4c8664cb *man/collapseClones.Rd
b1389cc1a3d3cab1d7a424f1e0093566 *man/createBaseline.Rd
49a7a21518ec93fe0f5d42f98b27e7ca *man/createMutabilityMatrix.Rd
291078043a96c53414245a7e245510d4 *man/createMutationDefinition.Rd
e3eefd932cca9d511015287438a68be1 *man/createRegionDefinition.Rd
612cc6343fce06e0cf4d821596cb5c7d *man/createSubstitutionMatrix.Rd
55e9db243c04b84f7119d5320ce01148 *man/createTargetingMatrix.Rd
a80b6016e0809af266eccfabb4fda3be *man/createTargetingModel.Rd
f4ba057a283ccf3f9a9040805a104a71 *man/distToNearest.Rd
3e1854b4dfa7ea94fb84d8fc8b6ae2ae *man/editBaseline.Rd
eeb3c312d361c86ec08be2959bc2167f *man/expectedMutations.Rd
3e45c045bc5e8522938912aa6513e7a6 *man/extendMutabilityMatrix.Rd
92510a9afa61258fb8ec6fce367678eb *man/extendSubstitutionMatrix.Rd
deda2c9dc1ba60b00e3f749922752dee *man/findThreshold.Rd
67e492a46e79b12cdef259ca81c40490 *man/getBaselineStats.Rd
34d212a2ad15aa008786ac14d9a446c5 *man/getPlatform.Rd
80b4bf39e1a72c5c3f47d2af3a1ae237 *man/getnproc.Rd
74948e196280fe24ce2586aed345c639 *man/groupBaseline.Rd
a64599327530e7dd2e26c79dc2bf27ae *man/makeAverage1merMut.Rd
d3ad96cd8466448271e018d0774ebb44 *man/makeAverage1merSub.Rd
a421abd5d1b8546f15e2926a3d3d601d *man/makeDegenerate5merMut.Rd
f1e35fb60180aa5226b1ca07fab136c2 *man/makeDegenerate5merSub.Rd
5c137ef63008e49040fb72e0d5a928ae *man/minNumMutationsTune.Rd
9b719761579a3ef57686793ff1211e76 *man/minNumSeqMutationsTune.Rd
c3a3f806089c39b9a33b718060dab0cc *man/observedMutations.Rd
67edcd430865d3c399af03a19d3b09b9 *man/plotBaselineDensity.Rd
e0fee1aa64d63dd4886487ba4c8ab96f *man/plotBaselineSummary.Rd
ef5f408ce471f971634c818ed75d7453 *man/plotDensityThreshold.Rd
5de9d7fa33c6aaa947ce6a018054dbac *man/plotGmmThreshold.Rd
1b77a8f7e030450365ed5c35f93cfcad *man/plotMutability.Rd
80cd00856243c5dbfb50fd8b946fadf9 *man/plotTune.Rd
d172e5a22c5fd8fa46376e9092dd847d *man/shazam.Rd
189d5dddef9436868b8a0c5df4c6a650 *man/shmulateSeq.Rd
b56295d58b780bce387b3aec56504986 *man/shmulateTree.Rd
4dcdb117521ce07eb3a4df5684842517 *man/slideWindowDb.Rd
f0aa8aae1bb4f145b69190e2d11bb9fb *man/slideWindowSeq.Rd
ca2908e607a32a8df137fc89962605e0 *man/slideWindowTune.Rd
bef5a2f0be838f2640ede039c5d6c5fa *man/slideWindowTunePlot.Rd
047d3ff615aa6d37e3e0b25d0985c3dc *man/summarizeBaseline.Rd
cb53374bbba568369aa4c22044bd7d56 *man/testBaseline.Rd
fa559348ea1c62b9ff781eb8f4232071 *man/writeTargetingDistance.Rd
2218ce33605d0f7ea3e484af66d23b72 *vignettes/Baseline-Vignette.Rmd
637ad37b1c2042ca1a54f7edf3016892 *vignettes/DistToNearest-Vignette.Rmd
5701dc3e14b9afe4c57997afcf67f975 *vignettes/Mutation-Vignette.Rmd
1785012971a135beb456f26bb9d1c144 *vignettes/Targeting-Vignette.Rmd
