3644ba14e4c21565aa01067f2011d3fe *DESCRIPTION
02784592b294479769959b620c28eb3b *NAMESPACE
914b611859dfda308e375c78d0530d3a *NEWS.md
d0796f0ea2228d7871661d52c1c1d60e *R/Baseline.R
78d71681689686b54d140c6285b33e19 *R/Core.R
09ead9cb1b38cc86a9cd465c8b100b12 *R/DistToNearest.R
499c3e8d2f4bc7efb2b8dcd6b6ff3922 *R/MutationDefinitions.R
9cae772006747e5bc783f99c3102f947 *R/MutationProfiling.R
2d34ed089cde26f3156a6acfae3f1e22 *R/RegionDefinitions.R
682a31377b44e04827581a98e303c4ba *R/Shazam.R
70c8a531a5d1137a9e5cc444804ce131 *R/Shmulate.R
92b51b6717480b721ec97f43dec9860f *R/TargetingModels.R
1d821cc64741432266cc41d5995e2393 *R/sysdata.rda
4196e2b5e0222b5929c5c8be002289e1 *README.md
b6a6696c335e97404b2ff45b8fa7be8a *build/vignette.rds
a6d8e4bb225163a04252376b3b2fe3b5 *data/CHARGE_MUTATIONS.rda
13597652e61fec4478f242e85d1f3ba5 *data/HH_S1F.rda
649dc69d8463511dd447c5dc48e72b8b *data/HH_S5F.rda
90e5eaa6a08ef93e8b15b32df55c48f8 *data/HKL_S1F.rda
2399ca27a028ca901131d4da09b4196b *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
914fe6b6ac51d564ef2ba1f85bb85800 *data/MK_RS1NF.rda
3b6e2193e8ff4730e65aae52ddb77d03 *data/MK_RS5NF.rda
c9c22320df42880769b793bea91ded36 *data/POLARITY_MUTATIONS.rda
ffaafe98d3c5d5c9b31228c6fe6cca47 *data/U5N.rda
ae6ab7434ee43157d8e8b2921f223c85 *data/VOLUME_MUTATIONS.rda
f3b50c606aaca388ab4155ea3428f454 *inst/CITATION
3f47b3cdf74a5658f9a917387f0798c2 *inst/doc/Baseline-Vignette.R
717899918407b576072e293cb82b68b0 *inst/doc/Baseline-Vignette.Rmd
1e8d8c5010dcc42a048ce0ff47b1dc71 *inst/doc/Baseline-Vignette.pdf
ed9d2f51349208e40a2abf2638e5e2ec *inst/doc/DistToNearest-Vignette.R
1a2e55bd24e6a776c7e29bbb9289f747 *inst/doc/DistToNearest-Vignette.Rmd
3ae1f54f6dcd49463010e819cba908b5 *inst/doc/DistToNearest-Vignette.pdf
ef921b08e885fb34f2c9502390691bc8 *inst/doc/Mutation-Vignette.R
0a49fdc063c71c9c06d1b66742f3d532 *inst/doc/Mutation-Vignette.Rmd
f02aa1817f2dc25fb94c7204a1a383be *inst/doc/Mutation-Vignette.pdf
e379bbc65665235bc41fc4001230a750 *inst/doc/Shmulate-Vignette.R
ae8dfa57bfcd91c6ccfc731d4264f248 *inst/doc/Shmulate-Vignette.Rmd
29fdedf97c71ef6037727c050b4af4d2 *inst/doc/Shmulate-Vignette.pdf
e5726cb3abfecfdb3a34c667931ff630 *inst/doc/Targeting-Vignette.R
1785012971a135beb456f26bb9d1c144 *inst/doc/Targeting-Vignette.Rmd
d5312d336daeb7fd55549547d9b75347 *inst/doc/Targeting-Vignette.pdf
2f3cd7938f21d16f822d1a4b3785c2e1 *man/Baseline-class.Rd
4c9241edade6d91e3a06f28de4694078 *man/DensityThreshold-class.Rd
b32b0ad8b0c85610fc217a14f1db81b2 *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
c8190a8b12eecd89380c83473adf09b4 *man/calcBaseline.Rd
3c87ae7b0ce94cac367485861486196c *man/calcExpectedMutations.Rd
409b89dea44510972c71d5ca6b147c5d *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
69fe893c6603906aaaa5f1dceb532a5e *man/calculateMutability.Rd
3b46f448710eb9e23fe67bca7cc3b4e1 *man/collapseClones.Rd
e0279514aa45a2f2baaafeef1d3f56eb *man/consensusSequence.Rd
41a5bcabfb5abc12c063255a98744ab8 *man/createBaseline.Rd
2758befe1b23d5a4e39eb76ad24a52a6 *man/createMutabilityMatrix.Rd
291078043a96c53414245a7e245510d4 *man/createMutationDefinition.Rd
492ef3e940bf53f731ef9e5cba3a8653 *man/createRegionDefinition.Rd
ed614da32197d586199faf6216a96bb4 *man/createSubstitutionMatrix.Rd
55e9db243c04b84f7119d5320ce01148 *man/createTargetingMatrix.Rd
d1b5d40e8f300b5b2619d53917b2d7c6 *man/createTargetingModel.Rd
ed5e5eeebbe9512fdf0492dbd4a97105 *man/distToNearest.Rd
28f8d664d0e879b01b0c3a680506653a *man/editBaseline.Rd
5882b0f7dbde750513a14126f3df7fa9 *man/expectedMutations.Rd
9e56bc899a938d5c0000c274e20c37ee *man/extendMutabilityMatrix.Rd
92510a9afa61258fb8ec6fce367678eb *man/extendSubstitutionMatrix.Rd
d1f266773b544f4d18463cc3e847cf4a *man/findThreshold.Rd
c4a08927235f63aa67a88f6bf690f4e2 *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
a1cec572eaa4a1ff0bddbab2fb2484a1 *man/observedMutations.Rd
9ce414855b9b98619d71e23849c25e5a *man/plotBaselineDensity.Rd
547f76a261b033fbdc7f2d20ca2eb66e *man/plotBaselineSummary.Rd
5be7c5b619d81c1809935f4bd7c49b98 *man/plotDensityThreshold.Rd
596fb1cc20116e3bf6b6e320fd5c0587 *man/plotGmmThreshold.Rd
dd51d0355510732690a33bea5186ace5 *man/plotMutability.Rd
45aa62c283592929678b8796822f2ffb *man/plotTune.Rd
c270d1d156e11fc8d41c84698bc27efb *man/shazam.Rd
9c0257b68090dd22be54563d9a0d1526 *man/shmulateSeq.Rd
1381bdf00829740807efe8aa9321d892 *man/shmulateTree.Rd
9458572c3ff6f7db5b04373fdb4e2207 *man/slideWindowDb.Rd
f0aa8aae1bb4f145b69190e2d11bb9fb *man/slideWindowSeq.Rd
dd22f562db6540807c4b42a403cf52f6 *man/slideWindowTune.Rd
0a6e9a63813d58f2383d52fe98230a0b *man/slideWindowTunePlot.Rd
7673e512a37a3781db8f43385394c4ad *man/summarizeBaseline.Rd
3da13d2062a0fd14891c787e2507f2a4 *man/testBaseline.Rd
eb562fee7fda5169a426ea340a6a0dc3 *man/writeTargetingDistance.Rd
717899918407b576072e293cb82b68b0 *vignettes/Baseline-Vignette.Rmd
1a2e55bd24e6a776c7e29bbb9289f747 *vignettes/DistToNearest-Vignette.Rmd
0a49fdc063c71c9c06d1b66742f3d532 *vignettes/Mutation-Vignette.Rmd
ae8dfa57bfcd91c6ccfc731d4264f248 *vignettes/Shmulate-Vignette.Rmd
1785012971a135beb456f26bb9d1c144 *vignettes/Targeting-Vignette.Rmd
