eb0b205631137e06c28ea18f9f90bc27 *DESCRIPTION
27c5764599abbded5e480c688ed71eed *NAMESPACE
2f050e208eb0a4228c0c25f52abf4f4e *NEWS.md
155b9806a5b267a14e5ea332d364b720 *R/Baseline.R
e7dfd25258f92ae4d6e7f6bb48006cbb *R/ConvertNumbering.R
df12b5bd4073277a19f475fee9739c07 *R/Core.R
f31c2828e91a7c6fedc702dcac447023 *R/Deprecated.R
abe478ac2983a348d5298f0a473cdec9 *R/DistToNearest.R
fc1ca93e44b98d017ecfdde4f1b57ecc *R/MutationDefinitions.R
0617de4fd6f433d6dabba742b357a307 *R/MutationProfiling.R
361f7757cb0cba262541c706ce2ce9f4 *R/RegionDefinitions.R
8c613e94ae4de36223f2fa0213fdd23f *R/RegionsExtend.R
555cc017a54d3f0f8d84b0ac71c612a9 *R/Shazam.R
865102bd921dbd0c99a38c8ad734dba8 *R/Shmulate.R
dee7b4b4568450fea58ada84a0dae2c7 *R/TargetingModels.R
dc2c1550661649ba66322319bb965e07 *R/kedd.R
c175a455cf91007926d8b78113af8f73 *R/sysdata.rda
e4ac289a5d4753b7f9ca4462eca14fb0 *README.md
7080893e02c49cd296d4424b9be55069 *build/partial.rdb
d0a0f82fe6b9217e91c3c37202c65f3f *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
4713b40fb5a5c8dbbb3a553576bf8b83 *data/IMGT_VDJ.rda
ee7ff985764d385373f5db509bfcaf1f *data/IMGT_VDJ_BY_REGIONS.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
85bda22975f3c86f80d417a5e12cfa4a *inst/doc/Baseline-Vignette.R
d44e1b00d4951878d9e8feca01b4b215 *inst/doc/Baseline-Vignette.Rmd
86acf158273827d789118681d3ffdc74 *inst/doc/Baseline-Vignette.pdf
16b10a32f2314ba4c3d80e41814dc822 *inst/doc/DistToNearest-Vignette.R
845c71a27653bc52c41d69845c43e7ff *inst/doc/DistToNearest-Vignette.Rmd
74f942356b25cac336a72b5b9aafd9d4 *inst/doc/DistToNearest-Vignette.pdf
757e22ce501db41d3fd1e985ecbd91a1 *inst/doc/Mutation-Vignette.R
74d6ec5a3599249c2762cd8b1f31b958 *inst/doc/Mutation-Vignette.Rmd
4218ebcf1f6df07851622d5cac0a1dbe *inst/doc/Mutation-Vignette.pdf
1dbc6b81b597b3046d502911aa2b675c *inst/doc/Shmulate-Vignette.R
1b1b263798e3c690a45f8eac47ebf3f4 *inst/doc/Shmulate-Vignette.Rmd
39d20c8d18e57dcbde3a28d9eda83178 *inst/doc/Shmulate-Vignette.pdf
057557fea1d11f2a241e07188ecd23e7 *inst/doc/Targeting-Vignette.R
7fab2cd434427a8675437e9b0c951b60 *inst/doc/Targeting-Vignette.Rmd
e4633b5db02756e61f4b0520b92fadcf *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
47e947f7796022fe66f6bb95d06aafd1 *man/IMGT_SCHEMES.Rd
52ba6171ad460704b1d9157e9b23b923 *man/MK_RS1NF.Rd
fb4f48c2b4dce0daee89ba3ce5b303cd *man/MK_RS5NF.Rd
be91c489ac41ef19a5bf5c85d15de841 *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
77942a00353a374d788ff8cfd45a052f *man/calcBaseline.Rd
c382d48eb26974ccde0459b43aac1f7c *man/calcExpectedMutations.Rd
28671ff2fbb86a8bcc66e1ed52d0cc91 *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
dcfe2ba5015dd474fbae85b473e81152 *man/calculateMutability.Rd
ed377986d09d9a6876aae278a6b29bc9 *man/collapseClones.Rd
f27c2ed04762ffd506758c786c315569 *man/consensusSequence.Rd
3b59f03a0d4394b1d07b2a74b513753f *man/convertNumbering.Rd
4e0eb86d5e1b4fbf0253f3c292afa783 *man/createBaseline.Rd
1864d88f4828360df2e201e04f698502 *man/createMutabilityMatrix.Rd
2f17381316788a99b4c087c1d5eb4355 *man/createMutationDefinition.Rd
492ef3e940bf53f731ef9e5cba3a8653 *man/createRegionDefinition.Rd
0480e16901f4ceb4f94899df3cd13058 *man/createSubstitutionMatrix.Rd
078e1bb0aecb3764fe2861149f210dd5 *man/createTargetingMatrix.Rd
0f0e999821975d77ad1d094f8fd09369 *man/createTargetingModel.Rd
4be7651d82923aeb5f1d4b8f6f5a2e27 *man/distToNearest.Rd
6552e2b6c3c0f9d01b53fc83634e79f1 *man/editBaseline.Rd
ef77804b38d00811f4fac9f0943dfec5 *man/expectedMutations.Rd
67cbb2869a1763dbc426d0e955c6881c *man/extendMutabilityMatrix.Rd
ad87d67c4a882136c7afa28101a5b37c *man/extendSubstitutionMatrix.Rd
76d20cc31b9b808d505cf8e4466d05dc *man/findThreshold.Rd
ab315ca57e4255b74ae75cacab6a9387 *man/groupBaseline.Rd
a64599327530e7dd2e26c79dc2bf27ae *man/makeAverage1merMut.Rd
d3ad96cd8466448271e018d0774ebb44 *man/makeAverage1merSub.Rd
a421abd5d1b8546f15e2926a3d3d601d *man/makeDegenerate5merMut.Rd
f1e35fb60180aa5226b1ca07fab136c2 *man/makeDegenerate5merSub.Rd
5fcae87eb1a59f104efe578af61271d4 *man/makeGraphDf.Rd
78ae223253f6b1a272a846a881873e7d *man/minNumMutationsTune.Rd
bdc39e88e23f42333ad25601b30a6f00 *man/minNumSeqMutationsTune.Rd
da8d087656261ace366c8b452411d249 *man/observedMutations.Rd
c482f662702b56cc1cfa6a32da83e68c *man/plotBaselineDensity.Rd
92660620d7f16180cf0f5f997581997d *man/plotBaselineSummary.Rd
cf65429261fc48ae7b596ea422238d63 *man/plotDensityThreshold.Rd
767b693dd2766bce94522103c3bb3459 *man/plotGmmThreshold.Rd
dd51d0355510732690a33bea5186ace5 *man/plotMutability.Rd
ddbe84750a199843ac9db662d50596a9 *man/plotSlideWindowTune.Rd
19b78b8ada15f437337cc80339f96048 *man/plotTune.Rd
4d11abe48d8f5e735225cea8bc6de2f4 *man/setRegionBoundaries.Rd
d70cb61ef011a5da286c68a293b63259 *man/shazam-package.Rd
e946ccbbd09fe107e00855ce1e8746f5 *man/shazam.Rd
ab6c72f099c6fac7cb2c127428f58e16 *man/shmulateSeq.Rd
1b69477030e9204221b91d6e138f2259 *man/shmulateTree.Rd
4123b9d195ee930c6c2f924bf70a3295 *man/slideWindowDb.Rd
78e31167100053a36c81ad52b2362bea *man/slideWindowSeq.Rd
3e75858a9ea35d3b92bcd7a232da672e *man/slideWindowTune.Rd
ce64b1e2f08ee66a801b043abaa28a73 *man/slideWindowTunePlot.Rd
bfd73c6a8503f8b083a83e4dbdbe6047 *man/summarizeBaseline.Rd
16716625ffd26275f998d13c270e53cf *man/testBaseline.Rd
eb562fee7fda5169a426ea340a6a0dc3 *man/writeTargetingDistance.Rd
d44e1b00d4951878d9e8feca01b4b215 *vignettes/Baseline-Vignette.Rmd
af30a44291d1391fb0fd7e070291f8ac *vignettes/Baseline-Vignette.md
845c71a27653bc52c41d69845c43e7ff *vignettes/DistToNearest-Vignette.Rmd
74d6ec5a3599249c2762cd8b1f31b958 *vignettes/Mutation-Vignette.Rmd
1b1b263798e3c690a45f8eac47ebf3f4 *vignettes/Shmulate-Vignette.Rmd
7fab2cd434427a8675437e9b0c951b60 *vignettes/Targeting-Vignette.Rmd
