d2aa31d4387fa1d7d55dd14af809f7e4 *DESCRIPTION
ffa1efc24fbf1125a98e46b3e1dfd8cd *NAMESPACE
b77a85ad65876073356733a2d052b6b8 *NEWS.md
c7ef844aa085e5540549ad586dc4ee91 *R/Baseline.R
e7dfd25258f92ae4d6e7f6bb48006cbb *R/ConvertNumbering.R
df12b5bd4073277a19f475fee9739c07 *R/Core.R
f31c2828e91a7c6fedc702dcac447023 *R/Deprecated.R
b053976059cdff75aafc351ae0e43882 *R/DistToNearest.R
892f6bb1e1019f565c5bdf13f4ac505d *R/MutationDefinitions.R
d210d800ba5060836472c9d3c8c90f54 *R/MutationProfiling.R
361f7757cb0cba262541c706ce2ce9f4 *R/RegionDefinitions.R
04eb0e6b63d12db20032d8b3c6629baa *R/RegionsExtend.R
b400ff8453663b16d335ec565631007c *R/Shazam.R
865102bd921dbd0c99a38c8ad734dba8 *R/Shmulate.R
849db70a18c6fa32b09b7b13e8a3c477 *R/TargetingModels.R
dc2c1550661649ba66322319bb965e07 *R/kedd.R
c175a455cf91007926d8b78113af8f73 *R/sysdata.rda
e4ac289a5d4753b7f9ca4462eca14fb0 *README.md
fb8ea54e3885d2f00b670e08bfecfe3c *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
3826c758b2b5834a9382b3fcbabd2aa3 *inst/doc/Baseline-Vignette.R
f56732d1c073e69905b5d7268b908da3 *inst/doc/Baseline-Vignette.Rmd
82a5a9c5d5d4d96446c6f38b0598b29a *inst/doc/Baseline-Vignette.pdf
5dd05f63b4ac72bef1e2c3b82d171d13 *inst/doc/DistToNearest-Vignette.R
de4289945bdc8bdd9faa9083c7cc1900 *inst/doc/DistToNearest-Vignette.Rmd
b705fe1bdcfdb98bfc0bd21f4836a696 *inst/doc/DistToNearest-Vignette.pdf
cd427fd702054a12859598f8376bf2b0 *inst/doc/Mutation-Vignette.R
9339c5d2d2dd916708b5a66117a254b1 *inst/doc/Mutation-Vignette.Rmd
65e211dda9bea1720eec1fc69da741fa *inst/doc/Mutation-Vignette.pdf
b791bd26158541e68c33d0f9851a367b *inst/doc/Shmulate-Vignette.R
55515e374ce9c2dbe893e66c99f362d0 *inst/doc/Shmulate-Vignette.Rmd
b74849b0a7a23b67f03b2541e72eaf8c *inst/doc/Shmulate-Vignette.pdf
cc70c81fd5d75b0877d869e3074ba196 *inst/doc/Targeting-Vignette.R
0c85dd613680efeab93432246124c5fc *inst/doc/Targeting-Vignette.Rmd
7891b5e4236fdabe93de7b7b91a7cdb4 *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
291078043a96c53414245a7e245510d4 *man/createMutationDefinition.Rd
492ef3e940bf53f731ef9e5cba3a8653 *man/createRegionDefinition.Rd
0480e16901f4ceb4f94899df3cd13058 *man/createSubstitutionMatrix.Rd
078e1bb0aecb3764fe2861149f210dd5 *man/createTargetingMatrix.Rd
0f0e999821975d77ad1d094f8fd09369 *man/createTargetingModel.Rd
30636a595b9976ec9ea128334344bc2b *man/distToNearest.Rd
6552e2b6c3c0f9d01b53fc83634e79f1 *man/editBaseline.Rd
ef77804b38d00811f4fac9f0943dfec5 *man/expectedMutations.Rd
67cbb2869a1763dbc426d0e955c6881c *man/extendMutabilityMatrix.Rd
ad87d67c4a882136c7afa28101a5b37c *man/extendSubstitutionMatrix.Rd
f7bcff69fbfbdde9e5d3343078009e62 *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
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
f56732d1c073e69905b5d7268b908da3 *vignettes/Baseline-Vignette.Rmd
de4289945bdc8bdd9faa9083c7cc1900 *vignettes/DistToNearest-Vignette.Rmd
9339c5d2d2dd916708b5a66117a254b1 *vignettes/Mutation-Vignette.Rmd
55515e374ce9c2dbe893e66c99f362d0 *vignettes/Shmulate-Vignette.Rmd
0c85dd613680efeab93432246124c5fc *vignettes/Targeting-Vignette.Rmd
