ab847f0460f4791b35508aa2687514f7 *DESCRIPTION
58908f514e02e2e9f83f01cdeaec0cbc *NAMESPACE
f876d6935229209c5503313b77a6f5ec *NEWS.md
2ff28b656069b099a07011380ee4f684 *R/Baseline.R
ed797682566d4f5ea2e98e1a0c86d7ba *R/Core.R
f8e65f4048e496b6cd7e016fb0748325 *R/DistToNearest.R
499c3e8d2f4bc7efb2b8dcd6b6ff3922 *R/MutationDefinitions.R
cf63a98f2c87db2b204c6322c8f42b7f *R/MutationProfiling.R
2d34ed089cde26f3156a6acfae3f1e22 *R/RegionDefinitions.R
f6d9d2d1cc2edc810f6773028894adab *R/Shazam.R
cae835aa4ac9c88c505397d5a8840b52 *R/Shmulate.R
d62a1df6e39307fe99e1e6dc279791e5 *R/TargetingModels.R
1d821cc64741432266cc41d5995e2393 *R/sysdata.rda
4196e2b5e0222b5929c5c8be002289e1 *README.md
e5567e647add67e831e1829f81db8eca *build/vignette.rds
a6d8e4bb225163a04252376b3b2fe3b5 *data/CHARGE_MUTATIONS.rda
13597652e61fec4478f242e85d1f3ba5 *data/HH_S1F.rda
649dc69d8463511dd447c5dc48e72b8b *data/HH_S5F.rda
90e5eaa6a08ef93e8b15b32df55c48f8 *data/HKL_S1F.rda
2399ca27a028ca901131d4da09b4196b *data/HKL_S5F.rda
27d7bdb4a59fb7e157790b5df263a24e *data/HYDROPATHY_MUTATIONS.rda
0f9173b818adc04ebb9bb7fbf05f1f7e *data/IMGT_V.rda
ee256d4b39c91cf9a4ad1bc0734f94f5 *data/IMGT_V_BY_CODONS.rda
e52a16496673bd88d91e6c8ec03c8760 *data/IMGT_V_BY_REGIONS.rda
5be4fece58471da92c7e7b1594056034 *data/IMGT_V_BY_SEGMENTS.rda
914fe6b6ac51d564ef2ba1f85bb85800 *data/MK_RS1NF.rda
3b6e2193e8ff4730e65aae52ddb77d03 *data/MK_RS5NF.rda
c9c22320df42880769b793bea91ded36 *data/POLARITY_MUTATIONS.rda
ffaafe98d3c5d5c9b31228c6fe6cca47 *data/U5N.rda
ae6ab7434ee43157d8e8b2921f223c85 *data/VOLUME_MUTATIONS.rda
f3b50c606aaca388ab4155ea3428f454 *inst/CITATION
2b664862804b83e114fa5740023f6ef2 *inst/doc/Baseline-Vignette.R
717899918407b576072e293cb82b68b0 *inst/doc/Baseline-Vignette.Rmd
d232ba2fc66e8765588a59918b0f4042 *inst/doc/Baseline-Vignette.pdf
83dfc9ed400ce8bb91d0e0b1f7f03d82 *inst/doc/DistToNearest-Vignette.R
1a2e55bd24e6a776c7e29bbb9289f747 *inst/doc/DistToNearest-Vignette.Rmd
4cc9388077c309bf045e2f672b9ef866 *inst/doc/DistToNearest-Vignette.pdf
b6b832e21bd1732c584bd5150bd14ac7 *inst/doc/Mutation-Vignette.R
0a49fdc063c71c9c06d1b66742f3d532 *inst/doc/Mutation-Vignette.Rmd
147d6700c01c502002391e78ef342fac *inst/doc/Mutation-Vignette.pdf
dc826bf7139192f70209548589e21b10 *inst/doc/Shmulate-Vignette.R
ae8dfa57bfcd91c6ccfc731d4264f248 *inst/doc/Shmulate-Vignette.Rmd
854aa9155d05e1d2af1d0a1c2b45d66b *inst/doc/Shmulate-Vignette.pdf
7a94e409727fcb9cb0de4b8404244a4c *inst/doc/Targeting-Vignette.R
1785012971a135beb456f26bb9d1c144 *inst/doc/Targeting-Vignette.Rmd
4457b23ecf82892a99fcd5a4a79a1322 *inst/doc/Targeting-Vignette.pdf
2f3cd7938f21d16f822d1a4b3785c2e1 *man/Baseline-class.Rd
4c9241edade6d91e3a06f28de4694078 *man/DensityThreshold-class.Rd
b32b0ad8b0c85610fc217a14f1db81b2 *man/GmmThreshold-class.Rd
98f6d6aeaadf58389960f586c02b3882 *man/HH_S1F.Rd
d7cad825b7d37ca0c856b785bf892b5f *man/HH_S5F.Rd
a138d04fc9b94bda4d43f77c0c34f64f *man/HKL_S1F.Rd
9ea9a7a7240150a9f983975ce17348f5 *man/HKL_S5F.Rd
3bed0f6c41fc0993eadc80bb61b17750 *man/IMGT_SCHEMES.Rd
d1cf9c4e6bcd13ac03bee4022cca7dda *man/MK_RS1NF.Rd
5a0b0b68f073d362ed921d7ce2b6d302 *man/MK_RS5NF.Rd
b52702a03ac31b18ced1ff1a8236b367 *man/MUTATION_SCHEMES.Rd
13787752e7a8c6d36e4580366cb8be82 *man/MutationDefinition-class.Rd
37bdc51c60fd3366a48546265720756e *man/RegionDefinition-class.Rd
fe986f4d822323fe47c96dd07391be2d *man/TargetingModel-class.Rd
9bbb541c44b6ca3ee17d2ae8e1b03d31 *man/U5N.Rd
92cad0ec92a4ba75c5e845b2242d6c3e *man/calcBaseline.Rd
60f548e905b0173102a4aa2618031671 *man/calcExpectedMutations.Rd
4c6b037fb08e6721fbcf9bae52aad85d *man/calcObservedMutations.Rd
e360c5f55ef91279e0c90ace525c57d0 *man/calcTargetingDistance.Rd
9010abf369f367ea2abc0e9cadd7b81f *man/calculateMutability.Rd
7244fd08ee1058dd7d3f0f08afa2ff21 *man/collapseClones.Rd
b1389cc1a3d3cab1d7a424f1e0093566 *man/createBaseline.Rd
a82658ecc3bec7e0a40275f59b698d62 *man/createMutabilityMatrix.Rd
7aa55483be5633c99d0603555f7d8c28 *man/createMutationDefinition.Rd
aaedabe8af1dc3420dd935504b18753f *man/createRegionDefinition.Rd
8d6bf2c0cf418f157c18bc82f4758c4c *man/createSubstitutionMatrix.Rd
55e9db243c04b84f7119d5320ce01148 *man/createTargetingMatrix.Rd
58b9f7e1e5e7b5fd444f17dd353dcdb1 *man/createTargetingModel.Rd
833381df9739e7098309e9262152308d *man/distToNearest.Rd
28f8d664d0e879b01b0c3a680506653a *man/editBaseline.Rd
1b41dcea61bdc2a1bccd5e1b90184d68 *man/expectedMutations.Rd
9e56bc899a938d5c0000c274e20c37ee *man/extendMutabilityMatrix.Rd
92510a9afa61258fb8ec6fce367678eb *man/extendSubstitutionMatrix.Rd
8dc92acc4f3a562a72b8b419f51debb8 *man/findThreshold.Rd
28cf8a8d869e79e606d64d7cb6bf89d6 *man/groupBaseline.Rd
a64599327530e7dd2e26c79dc2bf27ae *man/makeAverage1merMut.Rd
d3ad96cd8466448271e018d0774ebb44 *man/makeAverage1merSub.Rd
a421abd5d1b8546f15e2926a3d3d601d *man/makeDegenerate5merMut.Rd
f1e35fb60180aa5226b1ca07fab136c2 *man/makeDegenerate5merSub.Rd
5c137ef63008e49040fb72e0d5a928ae *man/minNumMutationsTune.Rd
ad2ab10e1ca9d6fdfd3f46d4919f55a9 *man/minNumSeqMutationsTune.Rd
20f38f1b0de544b34844bc4e1787e23d *man/observedMutations.Rd
04836265cc98e4c9e2fb8be5d9156542 *man/plotBaselineDensity.Rd
5af190074cdd92b0b940d1a9d7eac73a *man/plotBaselineSummary.Rd
0c5072593ae66cb82a1aa541ed737370 *man/plotDensityThreshold.Rd
f4abd43ca254a704af0cefd518c14276 *man/plotGmmThreshold.Rd
d5c10093f26bf75018a5f746fd10cafd *man/plotMutability.Rd
f1f06618cffc6eda28fa05ed68a8194b *man/plotTune.Rd
d172e5a22c5fd8fa46376e9092dd847d *man/shazam.Rd
27b5720258a88df262d696f9b09c3e41 *man/shmulateSeq.Rd
8ea23af22ec5a263dab0f79503b71e39 *man/shmulateTree.Rd
4dcdb117521ce07eb3a4df5684842517 *man/slideWindowDb.Rd
f0aa8aae1bb4f145b69190e2d11bb9fb *man/slideWindowSeq.Rd
745460758bb728cbb5fd30a1793dbe25 *man/slideWindowTune.Rd
f40ab24771f4229359af52fb2c29287c *man/slideWindowTunePlot.Rd
a99857c7739d454d5b80bbb69cd3497b *man/summarizeBaseline.Rd
3da13d2062a0fd14891c787e2507f2a4 *man/testBaseline.Rd
eb562fee7fda5169a426ea340a6a0dc3 *man/writeTargetingDistance.Rd
717899918407b576072e293cb82b68b0 *vignettes/Baseline-Vignette.Rmd
1a2e55bd24e6a776c7e29bbb9289f747 *vignettes/DistToNearest-Vignette.Rmd
0a49fdc063c71c9c06d1b66742f3d532 *vignettes/Mutation-Vignette.Rmd
ae8dfa57bfcd91c6ccfc731d4264f248 *vignettes/Shmulate-Vignette.Rmd
1785012971a135beb456f26bb9d1c144 *vignettes/Targeting-Vignette.Rmd