d207e3e77f73390142f674c9e70ffe31 *CITATION
0fbc4b102849006c9eaffdbfd4bd4a01 *DESCRIPTION
f3c5f2fc38de8c2b94ffe1f95b6211e3 *INDEX
c9aea8861c8b68911c744b0dcc8a5b3f *Meta/Rd.rds
c1964afaa813fbfb70dc6150fbf9477d *Meta/data.rds
3116b09a69f681bcdc57557b4c235db7 *Meta/features.rds
b1f16ae4a2cf97cc114e0fe6bdbae3d6 *Meta/hsearch.rds
00043cdd95a5299420f26235f16b3eaa *Meta/links.rds
ab43b960873168c0310c9aa900d6e768 *Meta/nsInfo.rds
cd84e603d93326d1f4bea7e4d692e89a *Meta/package.rds
722cbb197e6413b6329efdabc5cd851e *Meta/vignette.rds
7c32c9dfbb0775c6401e7ecfb75bd5f2 *NAMESPACE
2a3a3ddace3057fb79a719d0bdd0499a *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/PureCN
78f245d8c1106c57288939b15c55d7c4 *R/PureCN.rdb
aa340ed8a97624dd13b4fc6e6854a995 *R/PureCN.rdx
96f375c72d93d3e64ec0adeccf99f194 *data/centromeres.rda
3b4e2220ba5f0c63aff21624ec8b4d7b *data/purecn.example.output.rda
920646d006bfb1b0cbdb7176b8edf5c4 *doc/PureCN.R
b7c6e06ad66faa2d4da54c65e006deca *doc/PureCN.Rnw
425aa407e90c3e150bdf0dd9752a9112 *doc/PureCN.pdf
c0eecde560493777c35f76f893bf3222 *doc/Quick.R
f549febc9b8056f50a9da6407beb895c *doc/Quick.Rnw
704fb7b39789e0be54e7fd82daee6df4 *doc/Quick.pdf
51a2335a5fe463776b4078e8a48c344a *doc/index.html
40f980a59aecec21ea28c0af53aa8112 *extdata/Coverage.R
c599bfe7ff7ee1cce5fba99a3531b71a *extdata/IntervalFile.R
f539432b94e20b171fd8e29f23187184 *extdata/NormalDB.R
fd252c57baea3bb8719dcc33dd044733 *extdata/PureCN.R
3e55f3cbacf0ade2c2a406f1ad3f51b7 *extdata/downloadCentromeres.R
7df758adaaf5b6d487ac22e4dba6c31e *extdata/ex1.bam
1888862b9d22ddb8ca663eabc41c78f0 *extdata/ex1.bam.bai
7ff3a77a583973ad739082fc7d327298 *extdata/ex1_gcgene.txt
3cde10782966a832047779d3d1294e46 *extdata/ex1_intervals.txt
2d0f1cac0072d9788882f2b3ebc591b0 *extdata/ex2_intervals.bed
ff600751c668406cf7c32e7362ce3899 *extdata/ex2_intervals.txt
fbe2d2fffd0dc64303686f11b5817883 *extdata/ex2_reference.fa
35fcb62fd46b593d1269e249174c30ff *extdata/ex2_reference.fa.fai
3b1ed770f9de08a67d73e260b6bc97af *extdata/example_cosmic.vcf.gz
cb4501c1bb40ad0b7af797f7a756d74e *extdata/example_cosmic.vcf.gz.tbi
04ed9c18809a807d427a5867ff56533c *extdata/example_gc.gene.file.txt
78d8aca0fe4427f63b85c6fdc3d9bdb6 *extdata/example_normal.list
a412992421727d291a7d65cc62cd5db8 *extdata/example_normal.txt
3b6c3ae906b6dd7c11f67e1713232926 *extdata/example_normal2.txt
bb5da3767dabbd7a51ae717fddfef7d4 *extdata/example_seg.txt
79937e90092e791bd91c7a045bd921e9 *extdata/example_tumor.txt
5d73baed8fb0ff5dad0a4bb2d55ef1a4 *extdata/example_vcf.vcf
efc17f1901c0090230be09f42bd24366 *extdata/test_coverage_overlapping_intervals.txt
bfd0490cc5a96329bb2b96fef852ddcb *help/AnIndex
bcf4f7a8127844a473c03ebbfc28f7e3 *help/PureCN.rdb
16f5fa5f2477234b41884a725ced9929 *help/PureCN.rdx
e31f0d5a4a3db9184f1012805a292602 *help/aliases.rds
95a674648811c67ed70c65e29ee98caf *help/paths.rds
ea9b10159863a787d7de98ee36782bc0 *html/00Index.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
5ded8873d2a461f807385b0a7be1acf2 *unitTests/test_autoCurateResults.R
c84963bf3235ff7ca648e93d71610999 *unitTests/test_bootstrapResults.R
6f20a2f0302672e8ff21170896220e6a *unitTests/test_calculateBamCoverageByInterval.R
b8bc1517b1aa2add5b009986ec471573 *unitTests/test_calculateGCContentByInterval.R
c4791dfd46f11b76c25ca2a6e35f9b45 *unitTests/test_calculatePowerDetectSomatic.R
e38772a6799ff2e2f8698ad5df99336a *unitTests/test_callAlterations.R
75a750a8ae0e764ba6fdce39651598b1 *unitTests/test_callAlterationsFromSegmentation.R
96f73d8dd402b97c1b15804603af0894 *unitTests/test_callLOH.R
a76fbe720991dfcf4ad23c1c13e62b75 *unitTests/test_correctCoverageBias.R
a2302e3d77988709f3b39149d88ef5c1 *unitTests/test_createCurationFile.R
bf233d99acc921bb0eb1acec7611bac7 *unitTests/test_createNormalDatabase.R
79fe43c23b4320247d672d44c40af1be *unitTests/test_filterVcf.R
fe0ef6aa55b09ff1ad76cb70c8a48798 *unitTests/test_findFocal.R
40653398faaf6811ccb86d8e09e53e36 *unitTests/test_getDiploid.R
9d0e4519dcc28185233823c1b7444e53 *unitTests/test_getSexFromCoverage.R
255ee68eb5c90a68608d0455328e2e5a *unitTests/test_getSexFromVcf.R
60be062342447dba0678b01b491f57b2 *unitTests/test_poolCoverage.R
a91bf4719756b6985214995b11792dfc *unitTests/test_predictSomatic.R
5a64438e6ba30f98ea5563279bea148a *unitTests/test_readCoverageFile.R
5c1299c443a5f5bfbe70728e31e5b106 *unitTests/test_runAbsoluteCN.R
6d151553df64eebcd7426da838ea1267 *unitTests/test_setMappingBiasVcf.R
96ca0d2e680ba59f973f402337e74286 *unitTests/test_setPriorVcf.R
