9235cd18228ba48e03d92d604fdef984 *DESCRIPTION
a715b143e1b2bcd794cf1ea5c10ac09d *NAMESPACE
a2b5ce0356693e8d017697282464a163 *R/annotate_extra.R
92be0fca03b263715f2b3ed186edd7c5 *R/class_definition.R
e46c8af67530e000b74cca4971272c14 *R/countBamInGranges.R
f0e980a4ab747d225d6be591b9ce19a5 *R/optimize_reference_set.R
f029ba2ec71b09f34c08f9f03a1ba20d *R/plot_CNVs_method.R
ea4629b20cce211553c3efc143e1f8b8 *R/tools.R
6490e64fdc1f3062c4f758754866213a *R/zzz.R
951d13ef9fc527891ac7116802b149f1 *build/vignette.rds
c6d5038520b7c538bd2fc3e41c306e56 *data/Conrad.hg19.RData
b2d529dc152cdfa5d21c8ff6ea36dea3 *data/ExomeCount.RData
d36e7f0d1af103b82d1859f9f7679d2b *data/datalist
c8a566bb63b33a8a3f69aefa4b9fcb83 *data/exons.hg19.RData
bc9610bfc361c3be990e6bd37b36103e *data/exons.hg19.X.RData
99e626c31adb824244ea1698e14b2a45 *data/genes.hg19.RData
5a629c11e352320d9c4dfdf80223ee13 *inst/doc/ExomeDepth-vignette.R
4b3419b14e34d5d942b276afbd2685d8 *inst/doc/ExomeDepth-vignette.Rnw
4ee1057ea8dbf6e834859f80e7e5907a *inst/doc/ExomeDepth-vignette.pdf
f4f61c0aba993a6b15f97d10314eccfc *man/AnnotateExtra-ExomeDepth-method.Rd
092d94a8440a885505da2371a8475992 *man/C_hmm.Rd
33cc5f0cfffd824322bc5df0f143f9bd *man/CallCNVs-ExomeDepth-method.Rd
7de3f4f513d30c88bd78f697f75c5c28 *man/Conrad.hg19.common.CNVs.Rd
525753f73f5070f7f49484aa228c822e *man/ExomeCount.Rd
e85e255ed35f75764cfe8a982cf0c071 *man/ExomeDepth-class.Rd
0365849f9d8230e2282e52c17ba4ef47 *man/TestCNV-ExomeDepth-method.Rd
b6302df8a82de2ed66eb15d55dd71fe6 *man/count.everted.reads.Rd
6c40d4b9c33bcb7918d402bb7f0c844b *man/countBam.everted.Rd
6bbf082a0e5633f95d82f015d46d2edf *man/countBamInGRanges.exomeDepth.Rd
6bb2952d293e6670f041d34225336499 *man/exons.hg19.Rd
48356ed9c84a7c0ae1ca243aa065daa9 *man/exons.hg19.X.Rd
d7a8f8bd66b23ec9b544a4ccf297ff74 *man/genes.hg19.Rd
ad236d01100de9f3c3e6767633a3dfc7 *man/get.power.betabinom.Rd
ec7c3784f84c116da5fc175292825fd6 *man/getBamCounts.Rd
f32468b13d6bf2677c98339ec0dfbca2 *man/get_loglike_matrix.Rd
d700eb55ec8dcea59159aff2ec4b7044 *man/initialize-ExomeDepth-method.Rd
8de1e5f02d00d17867d8f45bdac6e6f7 *man/plot-methods.Rd
f24f1f102326b27c32e6846cb4ffaab3 *man/qbetabinom.Rd
ebd620de4b58155406384aa3fab6d315 *man/qbetabinom.ab.Rd
752186dc9ac25780fa428f85b592e1fb *man/select.reference.set.Rd
7023cb3a32ea0ca7492285dd93620d1b *man/somatic.CNV.call.Rd
12668ce160d99c4699f587da4439d9d5 *man/viterbi.hmm.Rd
642a39f32c711b9412366cd72940d6f6 *src/CNV_estimate.cpp
f7c222a1306729705639b5a66bea92a3 *src/ExomeDepth_init.c
739b77a79f61cc6cb8636f483116a2bf *src/VP_gamma.c
4329673448f171617bb1f1a64bf19248 *src/VP_infnan.c
3bd0c6339dc2748e8ecf089676e2e11f *src/VP_log.c
a0f44986b2615f9c2b622e712527c5e6 *src/VP_psi.c
091be3243a263ab4d507f288dc56094b *src/VP_trig.c
2f755ac0ed4f34f2c7d57ff99e12891f *src/VP_zeta.c
bfa702a0ef331ca8364f476029cf5a62 *src/beta.c
882f797c9e6fca45db18edc4518f2b63 *src/chebyshev.h
e05e8cf4ab4ca01770bc70c61a4e1f2a *src/check.h
747e59c537e2444ffed279d846c1f417 *src/config.h
9ee0a176bf972c19fcf4de7b92b9a23b *src/elementary.c
2257309e32c9c7954d937184882f8c3f *src/error.c
dca50d2be58e2b886fd15af87c021ae3 *src/error.h
9cc7ad31458854bf6da860f6bfcbfc0d *src/eval.h
03ac1b61690b0681a7f70786e5c9c052 *src/exp.c
c3ce4618a7c4ea3e869dbdc83de88a8d *src/fdiv.c
2e741f853b9325834974643ec6967c74 *src/gsl_complex.h
53bc1cedcd68d299c3a9c6fd4ead12f3 *src/gsl_complex_math.h
29375e97c3e838b00db8ac369a71c217 *src/gsl_errno.h
be30aed9e92a6bdbc56c9c89d8df15de *src/gsl_inline.h
5972b8a376cb0b1ab60ac2010adf16c1 *src/gsl_machine.h
f1602148097b13cd618543849f838664 *src/gsl_math.h
5f6e2472747d7a9e3e7d1c5dfb10cf6b *src/gsl_message.h
a2ad334362e058b65d64b966027397e6 *src/gsl_nan.h
044c7b14dca2e0714f8313c9d96f81a1 *src/gsl_pow_int.h
02bed4276da7d7ea3857a55b66040d04 *src/gsl_precision.h
002d93ed0c482ea27075c67708a69c60 *src/gsl_sf_elementary.h
1e16839c63be9cae389bfa0175be3b46 *src/gsl_sf_exp.h
d9cb21f9e4576cd07593c32554482aec *src/gsl_sf_gamma.h
9cde5eaf75787c256f7241998bfbec62 *src/gsl_sf_log.h
e731e0015a810e10a708fd21e63ffb7d *src/gsl_sf_pow_int.h
60d47376fadfca93ddb6528613379e77 *src/gsl_sf_psi.h
5b52deed011f1ffd07977b19a388d251 *src/gsl_sf_result.h
286b94b03c8d4d69ed1058311f74235c *src/gsl_sf_trig.h
a634b3995f8b5d2b50aa8440e5568ee7 *src/gsl_sf_zeta.h
98a1bc2048bfef2908db94d1e06ff81a *src/gsl_sys.h
bda32c1d76324b58e3c9f12cd0215850 *src/gsl_types.h
fd5c21b122661b0eede120f1e217ccac *src/hmm.cpp
20fb36ade795f1ad6673acab0d0da109 *src/hypot.c
2f876b0c63aa79cc5f78b4ebc631fe75 *src/invhyp.c
9b2c42911593ca03f3d41cfd03bc3632 *src/ldfrexp.c
c5c0d5946bc875288b18b0b6a79d77d4 *src/log1p.c
97d3d5ccb1fd0a9d8939d44126400117 *src/math.c
7c29496ab57de6d6ed92c32e14aa6bc8 *src/stream.c
4b3419b14e34d5d942b276afbd2685d8 *vignettes/ExomeDepth-vignette.Rnw
