f3b49bee41137ad168785cff123ed81e *DESCRIPTION
cda61d29626b4daf237418f7e8ab935b *NAMESPACE
bb53fc5ab11e8860d5854b2f5e77a5c6 *NEWS.md
c11c08f46a1a029388048b7842f6aa0e *R/Baseline.R
e7dfd25258f92ae4d6e7f6bb48006cbb *R/ConvertNumbering.R
5bac325bfa4d2aa36d00542e04c2c288 *R/Core.R
99677c8cca53f60b6e5fa70a877b58f5 *R/Deprecated.R
4b8f6d8fc0fbaa4d0d43f12e2efd61f6 *R/DistToNearest.R
fc1ca93e44b98d017ecfdde4f1b57ecc *R/MutationDefinitions.R
b3e4aba4c87bcd0ee513bad4009edc63 *R/MutationProfiling.R
07c138b28449a678284e6d74f1bcb9ba *R/RegionDefinitions.R
bea0cc49d501aafdf43b73f90ed1e7b8 *R/RegionsExtend.R
e6243b906759feb2df2e1ba505a69ad0 *R/Shazam.R
27eeab82bdaa3f141dfd8077b7e218ec *R/Shmulate.R
cf2bc7cf45b746209f0196624c1f20b1 *R/TargetingModels.R
dc2c1550661649ba66322319bb965e07 *R/kedd.R
c175a455cf91007926d8b78113af8f73 *R/sysdata.rda
7dece7f6232e42175422f48a79044d57 *README.md
af3401175684b1e7ff4b3d3b8941c6eb *build/partial.rdb
d93419b8bd356ca69ef0133200951ff2 *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
b528665c7d3474902f566c07ce7a326b *inst/CITATION
417b2a866e60207c96602207b2cb5692 *inst/doc/Baseline-Vignette.R
3569b797ef162bc4f60c51517043d118 *inst/doc/Baseline-Vignette.Rmd
a400c925aa22d3ca0f09a9cb18cc1046 *inst/doc/Baseline-Vignette.pdf
9197a3d234f9dee793aa3c24c1464c9e *inst/doc/DistToNearest-Vignette.R
0aa159da384714dbc58924a49e35af25 *inst/doc/DistToNearest-Vignette.Rmd
9c2194f4911ade796bc41700db531ffa *inst/doc/DistToNearest-Vignette.pdf
ffc7c035da1ad0461503eb22ed8bdc88 *inst/doc/Mutation-Vignette.R
db9bdffe23d9af2c98db95ba5c7a8650 *inst/doc/Mutation-Vignette.Rmd
b420d10b6b0b5f1fa4c414f2a067f3e2 *inst/doc/Mutation-Vignette.pdf
1dbc6b81b597b3046d502911aa2b675c *inst/doc/Shmulate-Vignette.R
75cfd7e55a2a0bc5546aa959c1d91c73 *inst/doc/Shmulate-Vignette.Rmd
aa34437a0de16aef2338004d6a954c1c *inst/doc/Shmulate-Vignette.pdf
56532cf08f4e0c8bb92140f2279ebdb2 *inst/doc/Targeting-Vignette.R
48ea864141d6cb8abad8cb5f9f2d34f6 *inst/doc/Targeting-Vignette.Rmd
070fe466a1cba090e65c3a8449f1e8fa *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
77942a00353a374d788ff8cfd45a052f *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
3b59f03a0d4394b1d07b2a74b513753f *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
03a3fffa786c6cbf17783b5d60f2650c *man/distToNearest.Rd
6552e2b6c3c0f9d01b53fc83634e79f1 *man/editBaseline.Rd
a46d913429cc4352099cf3dd3d675720 *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
36a63a979c83f7e3e73a0323337a12f6 *man/observedMutations.Rd
7b6d437610ec16f58db3de7dca9f413f *man/plotBaselineDensity.Rd
4986e7670cd1fe0dd0115b10df2b1ec7 *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
28dcfbb38c9cd3aecc38597d0d5c1e4c *man/shazam-package.Rd
451af1556a4d4c9819c5cd4dbcf6117d *man/shazam.Rd
06d099d927f68ef77171260c4cdce6ad *man/shmulateSeq.Rd
1b69477030e9204221b91d6e138f2259 *man/shmulateTree.Rd
4123b9d195ee930c6c2f924bf70a3295 *man/slideWindowDb.Rd
78e31167100053a36c81ad52b2362bea *man/slideWindowSeq.Rd
3e75858a9ea35d3b92bcd7a232da672e *man/slideWindowTune.Rd
e6f1118cc8b0119d2ff8add9d98ef45a *man/slideWindowTunePlot.Rd
bfd73c6a8503f8b083a83e4dbdbe6047 *man/summarizeBaseline.Rd
b5c420e1306da4c455d2ff1953e528bb *man/testBaseline.Rd
eb562fee7fda5169a426ea340a6a0dc3 *man/writeTargetingDistance.Rd
3569b797ef162bc4f60c51517043d118 *vignettes/Baseline-Vignette.Rmd
0aa159da384714dbc58924a49e35af25 *vignettes/DistToNearest-Vignette.Rmd
db9bdffe23d9af2c98db95ba5c7a8650 *vignettes/Mutation-Vignette.Rmd
75cfd7e55a2a0bc5546aa959c1d91c73 *vignettes/Shmulate-Vignette.Rmd
48ea864141d6cb8abad8cb5f9f2d34f6 *vignettes/Targeting-Vignette.Rmd
