c4c522da31a27925ea32c3312317c67e *DESCRIPTION
e096c80e50b90520bbd9b8ac19805a4c *NAMESPACE
e95f0ab7b14aab4a3b22891522803c2f *R/betabinom.R
2dbcb1bc52d1e2c243c4b6993a8bb5aa *R/deepSNV-class.R
020d2b2d9255390a892b55078eb8d2da *R/deepSNV-experimental.R
c5d33e493b6b0fb4720473e61a8b63a1 *R/deepSNV-functions.R
3f60f677ea73bb03ad5c366f7f669b58 *R/deepSNV-generics.R
9c89b5900ed94db1673a5111897d388d *R/deepSNV-methods.R
d7e0b54e2aadc5f5a68c29d884d100ae *R/deepSNV-misc.R
9651a321476a47af7d5fdd24b5af2811 *R/deepSNV-package.R
fecea1b4c1cf10beed467f74b61e1143 *R/shearwater-functions.R
fd655d35dcf95ee4d18437789379ead1 *R/shearwaterML.R
7e36d18848c824f5db233e3832a56bb0 *README.md
2157770016df9c629e63a060023fff8c *build/vignette.rds
3ccecc236923abcec5bf3979f95058ec *data/HIVmix.RData
e5e59d311d41716d436bda6c12d6b6f8 *data/RCC.RData
44fe941582b98ed2fb74a2ff43bd04dc *data/counts.RData
8f473e99da6aea7893fbf4f0967161a5 *data/phiX.RData
39946182d2a7087db51be00e27bfe68e *data/pi.RData
a198b59b439c25594d85e0f8c8afc300 *data/trueSNVs.RData
97d1cb27e8478d7ae4de59a2de8c86e7 *inst/CITATION
22cb13d61ad7ff19b6188aec288f2a93 *inst/NEWS
eb93e43e868cf6b00523766e2093961c *inst/TODO
bdce9542f85039294f3238cd7138421b *inst/doc/deepSNV.R
79ea907278cca8011a87b7954bfc02ce *inst/doc/deepSNV.Rnw
fb6473f2d1fa9dc459fe03e65b62cf12 *inst/doc/deepSNV.pdf
54d367cd8b44cdb9149572ec1942d977 *inst/doc/shearwater.R
fc4e56aed626edbec5e35a7c0ac725b0 *inst/doc/shearwater.Rnw
2e07eab68274a484b8af34051f6c3ba5 *inst/doc/shearwater.pdf
b7cad0a8151f8a008a8d938a286b7228 *inst/doc/shearwaterML.R
866271256074ead132c1e1225b663bac *inst/doc/shearwaterML.Rmd
f157fdcb11b68322fb2bee2bf07e685f *inst/doc/shearwaterML.html
03adcf464008b8e2642cdb62807764d3 *inst/example/deepSNV-example.R
f3dd841413d42161102b4b371b8b8e8f *inst/example/shearwater-example.R
62e3352bca95588f9d1478ae36f1ed83 *inst/extdata/control.bam
a3507164d703e922651e0e56236bc293 *inst/extdata/control.bam.bai
9f9a82a95852ae5a1150280604b78693 *inst/extdata/deepSNV.vcf
a04b4031bdc04278cb65173c35999698 *inst/extdata/shearwater.vcf
726e8a03994c95b6598305bedf578845 *inst/extdata/shearwater2.vcf
974e693f6dd19be388650d9ef95edb2c *inst/extdata/shearwaterML.vcf
6af3a3077f6d4ab936e1bb777ad8e910 *inst/extdata/test.bam
74ceb014e38fe7f5111bc9d501889a5e *inst/extdata/test.bam.bai
9d2b44ee633d2cfb839a7bff7b711201 *man/Extract-methods.Rd
559453470dc55cb36a25ebd38f126c02 *man/RCC.Rd
01ea2d2c9c8ebbab2e453f183bf7e036 *man/RF.Rd
e1d47e58dfa01358ce81f4899d96b1fa *man/bam2R.Rd
30a4b4efbc70a37da52c7647f7a0234f *man/betabinLRT.Rd
85fcba148b9c598cfb47c0ad5753b2eb *man/bf2Vcf.Rd
e258042fc0709124ac6e5c52557a6b21 *man/consensusSequence-methods.Rd
6fa8100828c46e5c67354f0a6d12fa8a *man/control-methods.Rd
403c7061d9729fdce7d7ae7c970a29c9 *man/coordinates-methods.Rd
a69a5687b171be314ef2f7d043f70f4c *man/counts.Rd
826b67c91bac87ec0e4f5b394570a4a8 *man/dbetabinom.Rd
e2504a80f4c1318b0152c697de123501 *man/deepSNV-class.Rd
e8a3920e72713d5243e312d50e8772ab *man/deepSNV-methods.Rd
9194b562dcca2eef0a7f5240e1b32e76 *man/deepSNV-package.Rd
f32bf613e775f296a52b41b3ccc520f5 *man/estimateDirichlet-methods.Rd
e6fb84b6197c6f90e2060eb718fa1a23 *man/estimateDispersion-methods.Rd
371fc9f12c12308aaa8b2bd388bfdcbe *man/estimateRho.Rd
d5d6dcdce5ff3ee98689ffe018d18b3e *man/loadAllData.Rd
8f4350c3dc62546ff32d36cf808077f2 *man/makePrior.Rd
3da5de09cfb13dfa46236747f481539e *man/manhattanPlot.Rd
67b44b04526891b79204365695c88fc5 *man/mcChunk.Rd
2a0d46603c23fef04264db4e5a0518c4 *man/normalize-methods.Rd
e099bd16e990d073106f8330b6863dd7 *man/p.combine.Rd
df8cf50abeaa559e0d111277cb1a4787 *man/p.val-methods.Rd
a51b153a600ce198fb89cb419f974c30 *man/pbetabinom.Rd
ec66c9f48ea6cf35447f91e23e636b20 *man/phiX.Rd
2a157bfb46ef3102d7bcb369a45ea09e *man/pi.Rd
1f1f934911ea727c6d59f1e2c9cd2420 *man/plot.deepSNV.Rd
4b8df82ee78c5f85b09a15b2d38fef0a *man/qvals2Vcf.Rd
f79fcba028c57082f86fa32ffb2c0a08 *man/repeatMask-methods.Rd
2c6c7b24e1bd3f181c4bfda5d6fc8c5d *man/shearwater.Rd
63d61725b1a7156b7ce8d13619384b65 *man/show-deepSNV-method.Rd
9c49b9d9de10d0b51cab3d6aa1abcdec *man/summary-methods.Rd
5dde7ff260dbc3a5843ef1773bb8e613 *man/test-methods.Rd
449816827e644ca43e9466ab4e79abe6 *man/trueSNVs.Rd
8f70f3059b16327b76dded1349b63512 *patches/NAMESPACE.patch
7b8d1c2c8939e293615971dd97729f83 *src/Makevars
1d7782134059478acd18af7b0fe1c547 *src/bam2R.cpp
c794aedc02e26b30468b8be0ff5965fc *src/betabinom.c
79ea907278cca8011a87b7954bfc02ce *vignettes/deepSNV.Rnw
fc4e56aed626edbec5e35a7c0ac725b0 *vignettes/shearwater.Rnw
866271256074ead132c1e1225b663bac *vignettes/shearwaterML.Rmd
