d207e3e77f73390142f674c9e70ffe31 *CITATION
063fbfde1c5ae0200d08975e07134bf5 *DESCRIPTION
5e035c33b96b78ea5d9c6997a22e3521 *INDEX
458f19958d12f23752f7896ed8a65a57 *Meta/Rd.rds
0976e8b3ad24ca68e511aa9cf9d9853b *Meta/data.rds
77a30dbd9a48297ae6e6ef2194a95267 *Meta/features.rds
de941f6f147ce38cd0f8eb2065bb51a1 *Meta/hsearch.rds
c17c11f2618cd648366ead603acb2168 *Meta/links.rds
3b8a2bdcc95e4cbb5bd2e07ececb74bd *Meta/nsInfo.rds
d0ce9356a46ae8bac3c1b99447bc9c37 *Meta/package.rds
773144c474b716ad489b1c4054eedd28 *Meta/vignette.rds
a02a374d2481b0f313dd1a337b17ae78 *NAMESPACE
a4d6b0c13daee55a24330d1765713b63 *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/PureCN
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cc51edf3758e59c410676c5182b72918 *R/PureCN.rdx
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346af3078a84dae224353d53bf1894d4 *data/datalist
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e5eec99c760102b6416b6461a49edffc *data/purecn.example.output.rda
e0a2616f362337a6faf88d3fbe48b12e *doc/PureCN.R
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1ae545918c436da92f18105464b0c593 *doc/Quick.R
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51a2335a5fe463776b4078e8a48c344a *doc/index.html
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06a4a654751be3eadf4e1b27ed7737ca *extdata/Dx.R
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1e5952cba079c04161b06e379c10ef1a *extdata/IntervalFile.R
5a02209e7b389f8acafd53bb87628399 *extdata/NormalDB.R
fa723612b12a203381db629d3c82f2a4 *extdata/PureCN.R
dc147e94ae2855d472787c9ce77eb530 *extdata/dist/calculateSbdry.R
3e55f3cbacf0ade2c2a406f1ad3f51b7 *extdata/dist/downloadCentromeres.R
7df758adaaf5b6d487ac22e4dba6c31e *extdata/ex1.bam
1888862b9d22ddb8ca663eabc41c78f0 *extdata/ex1.bam.bai
7ff3a77a583973ad739082fc7d327298 *extdata/ex1_gcgene.txt
3cde10782966a832047779d3d1294e46 *extdata/ex1_intervals.txt
3600e3733184b2cf5822b61d26114658 *extdata/ex2_intervals.bed
ff600751c668406cf7c32e7362ce3899 *extdata/ex2_intervals.txt
3182e4f35fef60cd6a0d9fdec742c79b *extdata/ex2_mappability.bed
e77fc2dcfc240ed02caf5f6d8cce5559 *extdata/ex2_mappability.bigWig
fbe2d2fffd0dc64303686f11b5817883 *extdata/ex2_reference.fa
35fcb62fd46b593d1269e249174c30ff *extdata/ex2_reference.fa.fai
132903c9cf51362b793d719a82500098 *extdata/ex2_reptiming.bed
9b97a8416ce0918d993be657b41ef8b9 *extdata/ex3_intervals.bed
bad94524668ccd54248551b63caf6d41 *extdata/ex3_mappability.bed
559ee8cb44c6df4fe00696181ef07c60 *extdata/ex3_reference.fa
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9242303d61055871f27ea41c01c1db36 *extdata/example_callable.bed.gz
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7cf6ebfc8d897064bdcd935830ef708d *extdata/example_intervals.txt
889cd6d608956276074287eef52e78d3 *extdata/example_intervals_tiny.txt
91e6bf7827f9f6de08942bcd9456a321 *extdata/example_mutect2.vcf.gz
f5c82a061425aff64204e05b5720a226 *extdata/example_mutect2.vcf.gz.tbi
78d8aca0fe4427f63b85c6fdc3d9bdb6 *extdata/example_normal.list
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15d982eb620d8f5cdf671c75d96b745d *extdata/example_normal3.cnn
9f8f7691886d943ef1e0e70ca00cabf0 *extdata/example_normal4.cnr
2a18a775c4d52d67095e83ffd9943f39 *extdata/example_normal5.hdf5
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bb5da3767dabbd7a51ae717fddfef7d4 *extdata/example_seg.txt
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98d086d895796257dc4c6a312773e222 *extdata/example_single.vcf.gz.tbi
79937e90092e791bd91c7a045bd921e9 *extdata/example_tumor.txt
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cfcfe0c54614686bd514ecafe41925c2 *extdata/example_vcf.vcf.gz
516302874424e3b8b8eaf5e45171da38 *extdata/example_vcf.vcf.gz.tbi
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d9676085e3af0a6e9847bf329e96e1be *extdata/normalpanel.vcf.gz.tbi
efc17f1901c0090230be09f42bd24366 *extdata/test_coverage_overlapping_intervals.txt
b62d923c6871798b5dab11489915b10c *help/AnIndex
85e245f80d2a693523cf464ee7f70b39 *help/PureCN.rdb
8a5aee99bea773c4fd8805e774d6d5d4 *help/PureCN.rdx
2e14523474ded9da378600cfd882f7f8 *help/aliases.rds
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854b716ea66b187a961181b0a9f45a79 *html/bootstrapResults.html
09372a5a8251c13a4e119b0aaad48d68 *html/calculateBamCoverageByInterval.html
5814488352580b96e0a801dc614d84f6 *html/calculateGCContentByInterval.html
787a0a8a4e2a278dbaf6834c57fbceba *html/calculateIntervalWeights.html
ea42b6ee21680f8024f7acfc887da253 *html/calculateLogRatio.html
657ce0ecd322149fe8483230782caf7f *html/calculateMappingBiasVcf.html
1772da87d0385efe5f85e395346f9b6a *html/calculatePowerDetectSomatic.html
356b35667e4cb228083ec4ad77d1eab9 *html/calculateTangentNormal.html
6888d062df25df27f21a88e031812c55 *html/callAlterations.html
557583d9e902b62fced40dd1f64f7244 *html/callAlterationsFromSegmentation.html
0e6a51080094f6b08526cdd4a32a183f *html/callLOH.html
7d0bc265707718cb9949914bbc9b9f66 *html/callMutationBurden.html
f3a50709232ffa92ab0001eab63811d6 *html/centromeres.html
da7439319e61e10e8cf0329220c36b3a *html/correctCoverageBias.html
fe188224d0eff29859ac1f132d6b96d7 *html/createCurationFile.html
aa3ff26cf0996b875aef0595fb82ab6d *html/createNormalDatabase.html
be76bf0b8ff21a81f0e95cae84a2c43f *html/createTargetWeights.html
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8459d095e0c6e05bb8f9e492fdfe2b76 *html/filterTargets.html
a425cf61b333b60e3314c366470cdee4 *html/filterVcfBasic.html
be8432a0c6f156262a45babdc7d20279 *html/filterVcfMuTect.html
fb33445a8385f71fce4b757b0067a51a *html/filterVcfMuTect2.html
339fd17a98cf7f60beaff489bcf5c331 *html/findBestNormal.html
afac89a60431f55545f6aa8973ecc477 *html/findFocal.html
7ecf2a94da514bf52ab34932aa5f0fcd *html/getSexFromCoverage.html
923a31f480838bbbd662b88a324e254e *html/getSexFromVcf.html
6b4aef157c28d541e6d54e3a310bffd6 *html/plotAbs.html
0a7b540d6c0dd9fd6e225a5bbdc9fb93 *html/poolCoverage.html
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830a10d28870824a8ea2bce4c3d61c70 *html/preprocessIntervals.html
7a0ab120691a703f20abcd290fd14aef *html/purecn.DNAcopy.bdry.html
af13f9f158167f04ce37e4f8abf7a4f2 *html/purecn.example.output.html
cc647cbf86833ca666f36d3064f63725 *html/readCoverageFile.html
25ff76c3909bca6cbbe33c26fd4b0ab5 *html/readCurationFile.html
02c81b8a0863cafa5c374c0a871e378c *html/runAbsoluteCN.html
0e65f90103c11584801f5fc43b84e81a *html/segmentationCBS.html
d8f6e39bdd4cb9620d61a9fe1ef131bb *html/segmentationPSCBS.html
d08cf550319b93ee84e3c87e963f2954 *html/setMappingBiasVcf.html
8468b36135a40c33407f381bcd8d7704 *html/setPriorVcf.html
