435544447217e08e53f7487eb056e400 *DESCRIPTION
b811035dec7e7913f1b1debe7f838fc3 *NAMESPACE
f3887ea07a03afed3c1533bbe36b868d *R/annotate_extra.R
e049fbe18d1c871915bb9883c41231e1 *R/class_definition.R
e2bc107845156e7fe336e87ed00fb5b0 *R/countBamInGranges.R
189b95cf6b40be398f099e541f765943 *R/optimize_reference_set.R
dfa81d299e4195afa191d303f2baa96d *R/plot_CNVs_method.R
74562225708d5e3f573c1b980cb9ab10 *R/tools.R
6490e64fdc1f3062c4f758754866213a *R/zzz.R
e3d2ccc0f60bf1a344633c81aa4e6b59 *build/vignette.rds
29116addffe63c795f8e763f8a2deabc *data/Conrad.hg19.RData
dc553fc5e7a38370751cb75520be4da7 *data/ExomeCount.RData
d36e7f0d1af103b82d1859f9f7679d2b *data/datalist
155e6f5a815af7731774c0fd8f163960 *data/exons.hg19.RData
3e15a53eef0e539d718dc53509f67fe1 *data/exons.hg19.X.RData
717582984d7f8d4bf181926920bc8b79 *data/genes.hg19.RData
d6350cf04d7fe693e02e4623dbd25053 *inst/AUTHORS
04de925d9979fb6b7213e25e811d5cd1 *inst/doc/ExomeDepth-vignette.R
61a183b9a0c86353e409e3c9697e8891 *inst/doc/ExomeDepth-vignette.Rnw
bc121921f837495bec3a17a18a066371 *inst/doc/ExomeDepth-vignette.pdf
a6a7ad64b42e2f7835c916375dda243a *inst/extdata/minimum_1_25630000_25650000.bam
c7ba52cd771cb2d16bec1871c79900ad *inst/extdata/minimum_1_25630000_25650000.bam.bai
4c048a6a82dcc9a2e7e838ce1ac90ca1 *man/AnnotateExtra-ExomeDepth-method.Rd
cff9f4330eae883b10d26eb4ea8bc0df *man/C_hmm.Rd
657c0eb61e83f913b7b5548bc2c43bf9 *man/CallCNVs-ExomeDepth-method.Rd
ee6da47d166a247e47cf2edeaae707bf *man/Conrad.hg19.common.CNVs.Rd
3672de91a755f59ed3f819236c40ffb9 *man/ExomeCount.Rd
91b5cca977467e0e899279a8c5752272 *man/ExomeDepth-class.Rd
a00b4d0a48a93744f4507dde1487a485 *man/TestCNV-ExomeDepth-method.Rd
233bdf5c99050d8dc7cba26ef4ac79bc *man/count.everted.reads.Rd
8550c20845009754c139f4d969746b35 *man/countBam.everted.Rd
a1173e657bbe9149432887bcc43ddc93 *man/countBamInGRanges.exomeDepth.Rd
16d19a26d46857175fe7761a5e51d5ec *man/exons.hg19.Rd
34ec7c2ef53d547d44906b8b62ee9ab3 *man/exons.hg19.X.Rd
d21ce21085328cf9de6a605eae6ba8d4 *man/genes.hg19.Rd
eb42e191fa04e9bb1afe209d1ea125ef *man/get.power.betabinom.Rd
74c741d05f41c42067ca98e9a5932443 *man/getBamCounts.Rd
6d1f163bfeb9584eaa94b0a97f76f5f3 *man/get_loglike_matrix.Rd
9efa8405dfe3be9bc77e0cb9f7a4cca3 *man/initialize-ExomeDepth-method.Rd
8de1e5f02d00d17867d8f45bdac6e6f7 *man/plot-methods.Rd
b701dc69a4faf6efaee0581f1fc393aa *man/qbetabinom.Rd
ebae9550a6caf0490fe843b9c80393db *man/qbetabinom.ab.Rd
ac939da6a5569dbfe6b35b48147e1b9f *man/select.reference.set.Rd
7023cb3a32ea0ca7492285dd93620d1b *man/somatic.CNV.call.Rd
91c86606923467ad564855783d320d88 *man/viterbi.hmm.Rd
642a39f32c711b9412366cd72940d6f6 *src/CNV_estimate.cpp
f7c222a1306729705639b5a66bea92a3 *src/ExomeDepth_init.c
d2495ee0d31fb0a97ece89a4b9413552 *src/VP_gamma.c
5df83536bd6dd99c1206f7e28bb61828 *src/VP_infnan.c
75ad96b7868eeb4a875c07ff2a55e2b8 *src/VP_log.c
9a9a081e22d7cbcccaef086e32870ab3 *src/VP_psi.c
d682306d056c0d258a2602630a4cad97 *src/VP_trig.c
5f56f7cab0faa424a7007d0bd329a04d *src/VP_zeta.c
535a463a2d11a7e11cdcda1187b3647c *src/beta.c
882f797c9e6fca45db18edc4518f2b63 *src/chebyshev.h
e05e8cf4ab4ca01770bc70c61a4e1f2a *src/check.h
8e3ac7c97421c33d2f231edad3c6145b *src/config.h
655a8711fff5e76ac8c6c952e6be0c98 *src/elementary.c
b961076580ac468c6a6f645db3f3b99c *src/error.c
dca50d2be58e2b886fd15af87c021ae3 *src/error.h
9cc7ad31458854bf6da860f6bfcbfc0d *src/eval.h
401fb34c4a3e76bf79c2005748f12a7c *src/exp.c
1bfacf2b0d06f60aaefc4fb58bb770a8 *src/fdiv.c
2e741f853b9325834974643ec6967c74 *src/gsl_complex.h
12851c9006e975c60ffcfc6123539078 *src/gsl_complex_math.h
29375e97c3e838b00db8ac369a71c217 *src/gsl_errno.h
be30aed9e92a6bdbc56c9c89d8df15de *src/gsl_inline.h
5972b8a376cb0b1ab60ac2010adf16c1 *src/gsl_machine.h
b9479f01223aeb0bfab4be9d3666fffd *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
ba4f2fd9ccad1a8ec07c02a6ec2f1e86 *src/hmm.cpp
f40b170720d363405770f3417b892acd *src/hypot.c
45254f730213be5a50bbbf6888ccb727 *src/invhyp.c
8e980d8cd05fee1c4c63c6439b5e33e3 *src/ldfrexp.c
d06f0436abe5adb2cac64be06634c8aa *src/log1p.c
07ca8d5e108b452afe35d6bb7edb1d03 *src/math.c
365b04ff1a96146e91afa3ad9299003d *src/stream.c
61a183b9a0c86353e409e3c9697e8891 *vignettes/ExomeDepth-vignette.Rnw
