d50aaddb9f3277f19439a01ad62c9d53 *DESCRIPTION
2547c9668cb73fc21657ce599a2f1789 *NAMESPACE
325513081227f013608e00e816c0b04f *NEWS.md
fc2cda72555bce29b32d7d5d8642148c *R/Baseline.R
2fdb3a9fc0ebcac9605d0f42c2180aa2 *R/ConvertNumbering.R
5bac325bfa4d2aa36d00542e04c2c288 *R/Core.R
b338cedb222b07771891ebfedd5b4e68 *R/Deprecated.R
bc57d4b0e14ba3f519a9d77e459b1c1a *R/DistToNearest.R
fc1ca93e44b98d017ecfdde4f1b57ecc *R/MutationDefinitions.R
c0d9d7989118126e00df77bcfcdfee9b *R/MutationProfiling.R
07c138b28449a678284e6d74f1bcb9ba *R/RegionDefinitions.R
bea0cc49d501aafdf43b73f90ed1e7b8 *R/RegionsExtend.R
6bee7c1de7a2a6bd0d824d92a890778d *R/Shazam.R
2a6c5f5be8bcb2a5e9f8142517d7a864 *R/Shmulate.R
324ae5075e22d7de3191baf2943d89e0 *R/TargetingModels.R
dc2c1550661649ba66322319bb965e07 *R/kedd.R
c175a455cf91007926d8b78113af8f73 *R/sysdata.rda
f7c16150dcacb297d02b1d5901a0532d *README.md
c5260b1bae00ec1fb8d54bd1b69b28ba *build/partial.rdb
e25011057e0c82fabebe08c2ab3e70bc *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
1acf5e41a3b7a7ae5ae4a75004422355 *data/U5N.rda
e19d67a1cd256df12aea9985917c0683 *data/VOLUME_MUTATIONS.rda
b528665c7d3474902f566c07ce7a326b *inst/CITATION
417b2a866e60207c96602207b2cb5692 *inst/doc/Baseline-Vignette.R
3569b797ef162bc4f60c51517043d118 *inst/doc/Baseline-Vignette.Rmd
d9ed9b72e6e806fb1d8bbda51412d197 *inst/doc/Baseline-Vignette.pdf
9197a3d234f9dee793aa3c24c1464c9e *inst/doc/DistToNearest-Vignette.R
0aa159da384714dbc58924a49e35af25 *inst/doc/DistToNearest-Vignette.Rmd
4f5e8862b273a1aa5c3efb77b095eb38 *inst/doc/DistToNearest-Vignette.pdf
ffc7c035da1ad0461503eb22ed8bdc88 *inst/doc/Mutation-Vignette.R
db9bdffe23d9af2c98db95ba5c7a8650 *inst/doc/Mutation-Vignette.Rmd
36f586d6bd7bba6a6fea3480b5f4c548 *inst/doc/Mutation-Vignette.pdf
be0708fecf2ea9deccba6c327fecd94e *inst/doc/Shmulate-Vignette.R
4d04f30b6f8f57e9f9d7a94c41340bf5 *inst/doc/Shmulate-Vignette.Rmd
848d18fd8b69717862213c1c34f9d53c *inst/doc/Shmulate-Vignette.pdf
56532cf08f4e0c8bb92140f2279ebdb2 *inst/doc/Targeting-Vignette.R
48ea864141d6cb8abad8cb5f9f2d34f6 *inst/doc/Targeting-Vignette.Rmd
1f38c1d7abe5e896db9da813f1fdf7f4 *inst/doc/Targeting-Vignette.pdf
d46f2bc80073e2fa14f8c6247cf5eba4 *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
86c91afaea2637c06ca480fbaa52c99b *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
039afebba93764e2d56dfe2e145c20b6 *man/TargetingModel-class.Rd
7fb9fdf190107b6241b7b226958c1861 *man/U5N.Rd
8827061f7788e20f4bb480259639149b *man/calcBaseline.Rd
c382d48eb26974ccde0459b43aac1f7c *man/calcExpectedMutations.Rd
8df2cc315dee03f503b8491d76e5d0d7 *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
dcfe2ba5015dd474fbae85b473e81152 *man/calculateMutability.Rd
28359b6e64f9fe62b57df3d4e8acb841 *man/collapseClones.Rd
f27c2ed04762ffd506758c786c315569 *man/consensusSequence.Rd
3c334a80bdd3da5e5dfbbc092faefca9 *man/convertNumbering.Rd
e9c44dc8c970a73a4df5ff33a9d92f74 *man/createBaseline.Rd
141ca65cb0eea272337efd7c70965613 *man/createMutabilityMatrix.Rd
2f17381316788a99b4c087c1d5eb4355 *man/createMutationDefinition.Rd
492ef3e940bf53f731ef9e5cba3a8653 *man/createRegionDefinition.Rd
d09cf369e11bd1a31afcc0ddaef49380 *man/createSubstitutionMatrix.Rd
078e1bb0aecb3764fe2861149f210dd5 *man/createTargetingMatrix.Rd
434cdd28d17f80cef12035e1010d138d *man/createTargetingModel.Rd
0ec0b13b6dd2964ee2b0317a1d385f9d *man/distToNearest.Rd
6552e2b6c3c0f9d01b53fc83634e79f1 *man/editBaseline.Rd
82d54c53aa5f7fef7d86aaa2f60725da *man/expectedMutations.Rd
67cbb2869a1763dbc426d0e955c6881c *man/extendMutabilityMatrix.Rd
ad87d67c4a882136c7afa28101a5b37c *man/extendSubstitutionMatrix.Rd
2a131f57b5e65f87eba328efeb251681 *man/findThreshold.Rd
a07f73f4f23c3d5d71742a86df722021 *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
8f6d69dd98dfea26e062dca9d3c51aa9 *man/observedMutations.Rd
7b6d437610ec16f58db3de7dca9f413f *man/plotBaselineDensity.Rd
4986e7670cd1fe0dd0115b10df2b1ec7 *man/plotBaselineSummary.Rd
cf65429261fc48ae7b596ea422238d63 *man/plotDensityThreshold.Rd
767b693dd2766bce94522103c3bb3459 *man/plotGmmThreshold.Rd
dd51d0355510732690a33bea5186ace5 *man/plotMutability.Rd
72a357dd77167ccb6f1849df03b4f664 *man/plotSlideWindowTune.Rd
19b78b8ada15f437337cc80339f96048 *man/plotTune.Rd
4d11abe48d8f5e735225cea8bc6de2f4 *man/setRegionBoundaries.Rd
612fdc0372a2f8262794530cd5f988c1 *man/shazam-package.Rd
13a2a7c3a7bf55ed5a2f37d3db4ab1ce *man/shazam.Rd
06d099d927f68ef77171260c4cdce6ad *man/shmulateSeq.Rd
7ac0eb6d967115b91cec1aa6a167e15c *man/shmulateTree.Rd
4123b9d195ee930c6c2f924bf70a3295 *man/slideWindowDb.Rd
78e31167100053a36c81ad52b2362bea *man/slideWindowSeq.Rd
dfe5bdd675d0d08898f67507541d9f14 *man/slideWindowTune.Rd
10d92be0c3a2d352e4daccfc7f355c13 *man/slideWindowTunePlot.Rd
bfd73c6a8503f8b083a83e4dbdbe6047 *man/summarizeBaseline.Rd
226a3d23dd8fce7a3826fa162d480424 *man/testBaseline.Rd
eb562fee7fda5169a426ea340a6a0dc3 *man/writeTargetingDistance.Rd
3569b797ef162bc4f60c51517043d118 *vignettes/Baseline-Vignette.Rmd
0aa159da384714dbc58924a49e35af25 *vignettes/DistToNearest-Vignette.Rmd
db9bdffe23d9af2c98db95ba5c7a8650 *vignettes/Mutation-Vignette.Rmd
4d04f30b6f8f57e9f9d7a94c41340bf5 *vignettes/Shmulate-Vignette.Rmd
48ea864141d6cb8abad8cb5f9f2d34f6 *vignettes/Targeting-Vignette.Rmd
