dd2872490fb339c9ccde9d8b357a4695 *DESCRIPTION
b6c1b0ac7e0104254c680a0430cfd6fb *NAMESPACE
15c555f0a6087636aec57eeaeb5d4ba5 *NEWS.md
ab1cf0944688b89f184cd6661a7a9a38 *R/Baseline.R
df12b5bd4073277a19f475fee9739c07 *R/Core.R
6003d08c6fd70be93849b3f48d4b91e1 *R/DistToNearest.R
0fd803b4af3c93992479c14469d9d3c6 *R/MutationDefinitions.R
9a8a3d00125d14367b961e352b5293e3 *R/MutationProfiling.R
5135c483ff18ab6b7b8f35dfe36b544f *R/RegionDefinitions.R
d9400a66b3e8854865dc00f24290320a *R/Shazam.R
03c438eef837d14f0d61e7b8f8e548ec *R/Shmulate.R
36a12810aed67d01e8b1288859e31b2b *R/TargetingModels.R
70059491eea793568ceb871bb52b3eb6 *R/sysdata.rda
4196e2b5e0222b5929c5c8be002289e1 *README.md
5266d10d407ca9b55f9ff87b670890b9 *build/vignette.rds
4f3f035add5dd931a91adcfba1b27baf *data/CHARGE_MUTATIONS.rda
13597652e61fec4478f242e85d1f3ba5 *data/HH_S1F.rda
a627e8ddc6ef887649482e4f51e39589 *data/HH_S5F.rda
90e5eaa6a08ef93e8b15b32df55c48f8 *data/HKL_S1F.rda
2b74df694e73995d484cec0792f36366 *data/HKL_S5F.rda
31b8bf981c581f80d98fa3cb961b40e4 *data/HYDROPATHY_MUTATIONS.rda
1d29e293a915c4d1f4706535f292329a *data/IMGT_V.rda
16e854af6aabf5ad793aeff99a2608ec *data/IMGT_V_BY_CODONS.rda
deb4ddac9b420d3197189f31c1da30f0 *data/IMGT_V_BY_REGIONS.rda
0c8d4a1f433678c4083485d780fcfe4b *data/IMGT_V_BY_SEGMENTS.rda
914fe6b6ac51d564ef2ba1f85bb85800 *data/MK_RS1NF.rda
c4a1bb3550fd6b5f81a14054add21cb0 *data/MK_RS5NF.rda
6133c0df8fe0735d20445d3c933a2df8 *data/POLARITY_MUTATIONS.rda
ffaafe98d3c5d5c9b31228c6fe6cca47 *data/U5N.rda
e19d67a1cd256df12aea9985917c0683 *data/VOLUME_MUTATIONS.rda
f3b50c606aaca388ab4155ea3428f454 *inst/CITATION
ac5d5f65765341266f9ae405aea76ff2 *inst/doc/Baseline-Vignette.R
84e20961b0492d618f0326073628bd11 *inst/doc/Baseline-Vignette.Rmd
ab1eae2626874cc1c0f8c4f85b5a3c81 *inst/doc/Baseline-Vignette.pdf
40de0ea50044217eda45e49de9079b0e *inst/doc/DistToNearest-Vignette.R
16e4dcc1f4f971ecce98abe9803aaa4e *inst/doc/DistToNearest-Vignette.Rmd
2dd984e335f02cbd2d6865108084d9e4 *inst/doc/DistToNearest-Vignette.pdf
cd427fd702054a12859598f8376bf2b0 *inst/doc/Mutation-Vignette.R
689458815c64ac5a5221877ae1607a10 *inst/doc/Mutation-Vignette.Rmd
1f3db4104b5e03e0e4184206c8388f57 *inst/doc/Mutation-Vignette.pdf
b791bd26158541e68c33d0f9851a367b *inst/doc/Shmulate-Vignette.R
5f9bbd89b49a9fc29d6f7a57d3757e20 *inst/doc/Shmulate-Vignette.Rmd
bf28df7dedca956f8a595da8f057fcd1 *inst/doc/Shmulate-Vignette.pdf
a759159a025a409c497ac761c93c5019 *inst/doc/Targeting-Vignette.R
e827f05023bfed5f00d4839ec992ec8b *inst/doc/Targeting-Vignette.Rmd
8bb85033ff8f233a6dbd29f3c41c79dd *inst/doc/Targeting-Vignette.pdf
ce614c872889c5489f8b5e376b1e03d7 *man/Baseline-class.Rd
4c9241edade6d91e3a06f28de4694078 *man/DensityThreshold-class.Rd
b32b0ad8b0c85610fc217a14f1db81b2 *man/GmmThreshold-class.Rd
d5a615ab4582a0e79e721a1ae62fcc66 *man/HH_S1F.Rd
223e7522518b67c36b628464b95a52dc *man/HH_S5F.Rd
fd6b00b1452d45467fcf48c64526a794 *man/HKL_S1F.Rd
27710dfa973ae1aa2714463afd1c706a *man/HKL_S5F.Rd
84f0a0e9af6e5f5b114512d94531d783 *man/IMGT_SCHEMES.Rd
52ba6171ad460704b1d9157e9b23b923 *man/MK_RS1NF.Rd
fb4f48c2b4dce0daee89ba3ce5b303cd *man/MK_RS5NF.Rd
8aad585a39b80d181561b4825c19c2bb *man/MUTATION_SCHEMES.Rd
0784db802d5b7527b49cca1214e5343f *man/MutabilityModel-class.Rd
13787752e7a8c6d36e4580366cb8be82 *man/MutationDefinition-class.Rd
b6395c818a08c84df5783fed5ab8c409 *man/RegionDefinition-class.Rd
61f1e2cccdb81bb8a0c0cce1a2480f18 *man/TargetingMatrix-class.Rd
5fb3a8e863923c3423319d03c4ca7da0 *man/TargetingModel-class.Rd
7fb9fdf190107b6241b7b226958c1861 *man/U5N.Rd
840bf499e5555c66bbc2530fc0742766 *man/calcBaseline.Rd
c382d48eb26974ccde0459b43aac1f7c *man/calcExpectedMutations.Rd
28671ff2fbb86a8bcc66e1ed52d0cc91 *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
dcfe2ba5015dd474fbae85b473e81152 *man/calculateMutability.Rd
3543b7420d19841f97a60cf9f68317b9 *man/collapseClones.Rd
9f9f8f83f14d766d1e728c3ef1af8f76 *man/consensusSequence.Rd
4e0eb86d5e1b4fbf0253f3c292afa783 *man/createBaseline.Rd
f1ddf397777553101c468250b869c69e *man/createMutabilityMatrix.Rd
291078043a96c53414245a7e245510d4 *man/createMutationDefinition.Rd
492ef3e940bf53f731ef9e5cba3a8653 *man/createRegionDefinition.Rd
7d11f1aee10dede25c1d81cb969fcf9e *man/createSubstitutionMatrix.Rd
da06534ed4a1ab6af435fc8556b03ac9 *man/createTargetingMatrix.Rd
76f3b619cf761d95cb37ecadc7230c7d *man/createTargetingModel.Rd
ffa660049d524d9c0f0d3db2e3fd86b1 *man/distToNearest.Rd
0f10a3bd11b7ef8fa9be4fe384d544d1 *man/editBaseline.Rd
32d62712f048f2a976728cc4719ad8d8 *man/expectedMutations.Rd
d7c9d0bcf61ddb5894afb400b84b8a97 *man/extendMutabilityMatrix.Rd
ad87d67c4a882136c7afa28101a5b37c *man/extendSubstitutionMatrix.Rd
0e2d0715d13b44812842c8e1db911272 *man/findThreshold.Rd
de6352d125ba818a4f31429f1220be1f *man/groupBaseline.Rd
a64599327530e7dd2e26c79dc2bf27ae *man/makeAverage1merMut.Rd
d3ad96cd8466448271e018d0774ebb44 *man/makeAverage1merSub.Rd
a421abd5d1b8546f15e2926a3d3d601d *man/makeDegenerate5merMut.Rd
f1e35fb60180aa5226b1ca07fab136c2 *man/makeDegenerate5merSub.Rd
3b3be58d2c5c40ca58c028f8a51e82e6 *man/minNumMutationsTune.Rd
94699556d289cd6dd2667c60b038662b *man/minNumSeqMutationsTune.Rd
69113eff7b05a5003c29dae82d563aef *man/observedMutations.Rd
622c0049dc0cc9dbf4eebeca555c151d *man/plotBaselineDensity.Rd
5e2f52216694d5f67f8e7482e24163e8 *man/plotBaselineSummary.Rd
cf65429261fc48ae7b596ea422238d63 *man/plotDensityThreshold.Rd
767b693dd2766bce94522103c3bb3459 *man/plotGmmThreshold.Rd
dd51d0355510732690a33bea5186ace5 *man/plotMutability.Rd
17095b8bfb1217af965e15a469bf7888 *man/plotTune.Rd
45a59dfb775ccfa34e09f05fa2f542e5 *man/shazam.Rd
ab6c72f099c6fac7cb2c127428f58e16 *man/shmulateSeq.Rd
1b69477030e9204221b91d6e138f2259 *man/shmulateTree.Rd
7ff7bbe22f652c8ea5ed2c6f752a7638 *man/slideWindowDb.Rd
9ee27a125bda5fd7a296641495d9de29 *man/slideWindowSeq.Rd
23ec6fab751b92a750df724f48f9b938 *man/slideWindowTune.Rd
0a6e9a63813d58f2383d52fe98230a0b *man/slideWindowTunePlot.Rd
820146be6dfcfe9b6f29bac411d48ba4 *man/summarizeBaseline.Rd
a347b3e7a51961a499586a701b9921f2 *man/testBaseline.Rd
eb562fee7fda5169a426ea340a6a0dc3 *man/writeTargetingDistance.Rd
84e20961b0492d618f0326073628bd11 *vignettes/Baseline-Vignette.Rmd
16e4dcc1f4f971ecce98abe9803aaa4e *vignettes/DistToNearest-Vignette.Rmd
689458815c64ac5a5221877ae1607a10 *vignettes/Mutation-Vignette.Rmd
5f9bbd89b49a9fc29d6f7a57d3757e20 *vignettes/Shmulate-Vignette.Rmd
e827f05023bfed5f00d4839ec992ec8b *vignettes/Targeting-Vignette.Rmd
