c0f905498586384959bd18fc5f3f3104 *DESCRIPTION
d88eaebc20ad46fd1b33f3c4f3564657 *NAMESPACE
cedc06240812cd7e6196235ce1b3b103 *NEWS.md
d17bb6658b9e6fd3a822d1fb6aec700d *R/Baseline.R
169fb4acc0e443470dab716e60fea3d0 *R/Core.R
909988f31697810642f3164e1726d3ab *R/DistToNearest.R
499c3e8d2f4bc7efb2b8dcd6b6ff3922 *R/MutationDefinitions.R
78f6e77f7655602936694384d7ce2bf3 *R/MutationProfiling.R
0d9ca2f914ebd7dd6c61c39069265baa *R/RegionDefinitions.R
e5fb47403322b31577431b47e8d08364 *R/Shazam.R
23b8b335c6648c9dcca333c6994f8cc4 *R/Shmulate.R
186bfc3053423ce0430378a2fc0c53b3 *R/TargetingModels.R
1d821cc64741432266cc41d5995e2393 *R/sysdata.rda
4196e2b5e0222b5929c5c8be002289e1 *README.md
be95bc7d649b414df962f4cb3807ceee *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
0f9173b818adc04ebb9bb7fbf05f1f7e *data/IMGT_V.rda
ee256d4b39c91cf9a4ad1bc0734f94f5 *data/IMGT_V_BY_CODONS.rda
e52a16496673bd88d91e6c8ec03c8760 *data/IMGT_V_BY_REGIONS.rda
5be4fece58471da92c7e7b1594056034 *data/IMGT_V_BY_SEGMENTS.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
7f7e2a069f071cc008599ea27d3b8860 *inst/doc/Baseline-Vignette.pdf
8b7c02df2a8df927928da6a0be4adeaf *inst/doc/DistToNearest-Vignette.R
81338d2a15d7826ce29d853060f90602 *inst/doc/DistToNearest-Vignette.Rmd
3dc06d3d14ba830e72e35ecae3675837 *inst/doc/DistToNearest-Vignette.pdf
b6b832e21bd1732c584bd5150bd14ac7 *inst/doc/Mutation-Vignette.R
0a49fdc063c71c9c06d1b66742f3d532 *inst/doc/Mutation-Vignette.Rmd
91034d234457b67885117bc291405d88 *inst/doc/Mutation-Vignette.pdf
dc826bf7139192f70209548589e21b10 *inst/doc/Shmulate-Vignette.R
0f9a94977e68a65eb0da81f5b1d4e1a4 *inst/doc/Shmulate-Vignette.Rmd
59fd1d8e03201ddccc421df5a39de687 *inst/doc/Shmulate-Vignette.pdf
7a94e409727fcb9cb0de4b8404244a4c *inst/doc/Targeting-Vignette.R
1785012971a135beb456f26bb9d1c144 *inst/doc/Targeting-Vignette.Rmd
285926c4f6ec654e873b5a1994e6eb1d *inst/doc/Targeting-Vignette.pdf
bdf3c40f1ad2693ec1a4ae1a380ec962 *inst/markr/build.R
e7da62d13c2f88e9a58565e97055db0d *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
3bed0f6c41fc0993eadc80bb61b17750 *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
fe986f4d822323fe47c96dd07391be2d *man/TargetingModel-class.Rd
9bbb541c44b6ca3ee17d2ae8e1b03d31 *man/U5N.Rd
8c6816de404b3f44da5f1a7fc118695c *man/calcBaseline.Rd
f7fe5e20697f92665982b293ec2ed96c *man/calcExpectedMutations.Rd
8cbc105d4fa29cb4ce77e3afafb8cdfa *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
9010abf369f367ea2abc0e9cadd7b81f *man/calculateMutability.Rd
0e531760f7839c686640b0319d814aaa *man/clearConsole.Rd
61d49889989a0be9fdc15df8f5da6404 *man/collapseClones.Rd
b1389cc1a3d3cab1d7a424f1e0093566 *man/createBaseline.Rd
8d0cd8cddbd1edbb7ff6f272e2e0c786 *man/createMutabilityMatrix.Rd
291078043a96c53414245a7e245510d4 *man/createMutationDefinition.Rd
e3eefd932cca9d511015287438a68be1 *man/createRegionDefinition.Rd
3b058c670c4f0dd1bf976f30d0778c53 *man/createSubstitutionMatrix.Rd
55e9db243c04b84f7119d5320ce01148 *man/createTargetingMatrix.Rd
2a8492e9404b9271e3547f3800e91167 *man/createTargetingModel.Rd
19476527e823a2d4344e47142779cb30 *man/distToNearest.Rd
c48aebad10772e16266ab6bf42e5a525 *man/editBaseline.Rd
1b41dcea61bdc2a1bccd5e1b90184d68 *man/expectedMutations.Rd
9e56bc899a938d5c0000c274e20c37ee *man/extendMutabilityMatrix.Rd
92510a9afa61258fb8ec6fce367678eb *man/extendSubstitutionMatrix.Rd
ee282cfe0789067d4820d3918ec4cd0a *man/findThreshold.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
a8f6d9977afdf73d6e2143e9c2cf9df7 *man/plotBaselineSummary.Rd
0c5072593ae66cb82a1aa541ed737370 *man/plotDensityThreshold.Rd
f4abd43ca254a704af0cefd518c14276 *man/plotGmmThreshold.Rd
d5c10093f26bf75018a5f746fd10cafd *man/plotMutability.Rd
b857609a88f4a8d6b394e1f9810ca19d *man/plotTune.Rd
d172e5a22c5fd8fa46376e9092dd847d *man/shazam.Rd
27b5720258a88df262d696f9b09c3e41 *man/shmulateSeq.Rd
8ea23af22ec5a263dab0f79503b71e39 *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
0a49fdc063c71c9c06d1b66742f3d532 *vignettes/Mutation-Vignette.Rmd
0f9a94977e68a65eb0da81f5b1d4e1a4 *vignettes/Shmulate-Vignette.Rmd
1785012971a135beb456f26bb9d1c144 *vignettes/Targeting-Vignette.Rmd
