d207e3e77f73390142f674c9e70ffe31 *CITATION
6d85cd6021ae12225fb24038f59159a4 *DESCRIPTION
01e4300c8f7e2f0d146dc415be05fb58 *INDEX
51685089628870e890b8dd5b661c55b3 *Meta/Rd.rds
9f18f9146e702829a68ce10548846d37 *Meta/data.rds
e00065855163c282e8adab2a116bf019 *Meta/features.rds
dbca61a0059282ca179c1c0f3a34ac63 *Meta/hsearch.rds
0946de9d7979fc6b802658b91477a7c3 *Meta/links.rds
a6697850e6bc7c0e69cfa0ad464b391f *Meta/nsInfo.rds
d3fad3ebbefb753e30a2a8eecb44f326 *Meta/package.rds
17cc8b479aba1f4b0fff9b8ab1212675 *Meta/vignette.rds
34627c1eb27686c3592552b7dec7ff50 *NAMESPACE
80fc7a7aeede9690b3c73a995e5a1897 *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/PureCN
839441601ef20e2d12a3ddc72b4f6fdc *R/PureCN.rdb
e3d733085e91f1494d5e74943f966106 *R/PureCN.rdx
c0a1abec0c9afac63f2d710015c543f1 *data/centromeres.rda
3b43e27c728d8531b64372cc8960bbf1 *data/purecn.DNAcopy.bdry.rda
367c28dba4fbe4a852a360055af9b65a *data/purecn.example.output.rda
ffc63d5f0059dcf066e36cc67419250e *doc/PureCN.R
3d3eb2b8f50b478b72561ec7358f6650 *doc/PureCN.Rnw
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523f2584c35f2c61a9801e43ad54fd16 *doc/Quick.R
aed5bfd86a3f914f6b66d427ad85e0b3 *doc/Quick.Rmd
803eadaa16d5a7b854f9d6fdbd93a32a *doc/Quick.html
ee1bc7921840742f0fc607763c45c233 *doc/index.html
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bbd14502d5f4bdb6e1a265374884ce03 *extdata/Coverage.R
baa21812a5c37660ba41043fa034341b *extdata/Dx.R
43d66236d3cb54652ce6a1f4bda15819 *extdata/FilterCallableLoci.R
bb7aebbe939a88b499a644eff74bca45 *extdata/IntervalFile.R
8a0dd74f05a8ada5a0a9ef8449e8363f *extdata/NormalDB.R
61041ce9be335713286ac30f31f9ba4e *extdata/PureCN.R
8212796045d23163776d02c9996f14a9 *extdata/buggy_cnvkit.seg.gz
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
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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
b9affa44c1486b4a1dfe8552bc60b25c *extdata/ex3_reference.fa.fai
68bc0e561bfdb009114f3587a4c84526 *extdata/example.vcf.gz
9242303d61055871f27ea41c01c1db36 *extdata/example_callable.bed.gz
3b1ed770f9de08a67d73e260b6bc97af *extdata/example_cosmic.vcf.gz
cb4501c1bb40ad0b7af797f7a756d74e *extdata/example_cosmic.vcf.gz.tbi
1c28b0038d8c843f938f3a77f9f34faf *extdata/example_gatk4_denoised_cr.tsv.gz
5de34022e616b42afeda6dacae8f3321 *extdata/example_gatk4_modelfinal.seg.gz
7cf6ebfc8d897064bdcd935830ef708d *extdata/example_intervals.txt
889cd6d608956276074287eef52e78d3 *extdata/example_intervals_tiny.txt
f1cebe205c20384962326e802c117cba *extdata/example_logratio.txt.gz
91e6bf7827f9f6de08942bcd9456a321 *extdata/example_mutect2.vcf.gz
f5c82a061425aff64204e05b5720a226 *extdata/example_mutect2.vcf.gz.tbi
78d8aca0fe4427f63b85c6fdc3d9bdb6 *extdata/example_normal.list
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3b6c3ae906b6dd7c11f67e1713232926 *extdata/example_normal2.txt
15d982eb620d8f5cdf671c75d96b745d *extdata/example_normal3.cnn
9f8f7691886d943ef1e0e70ca00cabf0 *extdata/example_normal4.cnr
2a18a775c4d52d67095e83ffd9943f39 *extdata/example_normal5.hdf5
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bb5da3767dabbd7a51ae717fddfef7d4 *extdata/example_seg.txt
ba6cdc51e670166d3932f7f66a3bc241 *extdata/example_single.vcf.gz
98d086d895796257dc4c6a312773e222 *extdata/example_single.vcf.gz.tbi
79937e90092e791bd91c7a045bd921e9 *extdata/example_tumor.txt
a26dff8621f71b83ce4ac5eee24e85ec *extdata/example_tumor2.txt
77d4c608f251f9ce95bfec040912cd2c *extdata/example_tumor_tiny.txt
cfcfe0c54614686bd514ecafe41925c2 *extdata/example_vcf.vcf.gz
516302874424e3b8b8eaf5e45171da38 *extdata/example_vcf.vcf.gz.tbi
c2cf4cd1c575357dede7a5f26780c2f4 *extdata/issue109.vcf.gz
65c0d0db29e9eb08431353421592bdfe *extdata/issue62.vcf.gz
5a9102d13b20c08bb5d40c1cfd905f9a *extdata/issue62.vcf.gz.tbi
edf609a37d88244a6c43b8d7a4e86c27 *extdata/normalpanel.vcf.gz
d9676085e3af0a6e9847bf329e96e1be *extdata/normalpanel.vcf.gz.tbi
efc17f1901c0090230be09f42bd24366 *extdata/test_coverage_overlapping_intervals.txt
c2e77bff4d4fb17d393d49995d86506f *help/AnIndex
164ed06c54451c96d1893706fd25f1bf *help/PureCN.rdb
98acf0ee6480d609913a7885c6d8aa64 *help/PureCN.rdx
c349412a1f8377672f9ea37fccc3ad65 *help/aliases.rds
bcdf4e29b3fb8b3d037a05067748d6ec *help/paths.rds
554f3f67d554c37277037816bf87b277 *html/00Index.html
884574d9ea3fcf5f2eee4ec3783bd5b3 *html/PureCN-defunct.html
9145629224d160aeba4d308d3988ff56 *html/PureCN-deprecated.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
4859264db5c9f4e5b7aa28f112264856 *html/annotateTargets.html
bf6039770f1931b7a9c2b80e811d4f3a *html/bootstrapResults.html
3f44bce5a7fb385512ee455e7c71b458 *html/calculateBamCoverageByInterval.html
2f2ddd7268268699764aedeb56c41c72 *html/calculateGCContentByInterval.html
725b33dc862b61d70b3db4e159723c5b *html/calculateIntervalWeights.html
d24767fab004fd9aa10b6e3b6f0ebc25 *html/calculateLogRatio.html
d3d347e622276c89490c4e031a2b8082 *html/calculateMappingBiasVcf.html
1b2925508f998f6a0c3df8c77cf0cf67 *html/calculatePowerDetectSomatic.html
fdabc289a7b76c30ffc380e1637f4350 *html/calculateTangentNormal.html
3e2c3df391ef425ceae5c389a07546c1 *html/callAlterations.html
d8eadf6ce242390e0ed45ebcd22ddd15 *html/callAlterationsFromSegmentation.html
3990cba8b58b6311e1dd99a207b30c69 *html/callAmplificationsInLowPurity.html
b35c297b68fcb3a5db439906e73730d6 *html/callCIN.html
2c585c2746e84d43bd806304f6005d5f *html/callLOH.html
895309f08150fcb99509149eb4922eb8 *html/callMutationBurden.html
4b7ec9a85433052e52276fb54a56316e *html/centromeres.html
47c2c64c2b96aad5dca4922f78c1a1a1 *html/correctCoverageBias.html
0cf2c30897c69bca2b50409a4f3649b8 *html/createCurationFile.html
efbdec9aedeba04e536bafb500f9e29d *html/createNormalDatabase.html
d2516d573b078be1062f8793f560341b *html/createTargetWeights.html
9bcb16ce9ac9056a0eb5e67bf6d5297e *html/filterIntervals.html
c6de44f3aad64bf712065318446c9646 *html/filterTargets.html
3c67fb14acc22eb88aaec6270b3b1abe *html/filterVcfBasic.html
ca39ee6e984920a3efbd8f8ae8fb6430 *html/filterVcfMuTect.html
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4b200a1b9e4a35139e97e6fc48f20f41 *html/findFocal.html
d4e0d1ae120621c429a84cf73a224c3e *html/getSexFromCoverage.html
9ab60f774b0c7c94ced766fb56934c5f *html/getSexFromVcf.html
2e80002649825daafda6847db4405b73 *html/plotAbs.html
69794dd9d294dbdf5359479a216ac65d *html/poolCoverage.html
6f755a3dde523402118b6c3f062ed0be *html/predictSomatic.html
58b21c3486ee64773b4c74442b355303 *html/preprocessIntervals.html
98206dcdff199515836133b9f3c3d10e *html/processMultipleSamples.html
93ace9695969fa716973c35942e5f8c4 *html/purecn.DNAcopy.bdry.html
c6a5b1be05ccc7b210ad2d584f563082 *html/purecn.example.output.html
a57867d2a0cd66674b971daf279f5ba4 *html/readCoverageFile.html
55b0f9e9fd94b9570ad760e71c054b21 *html/readCurationFile.html
07eb05cb6b21585a58da019548ac63ec *html/readLogRatioFile.html
27f3e71c445551304cc1c11c717ac945 *html/readSegmentationFile.html
5de9135d708bd2d966ec7c241cafa5d9 *html/runAbsoluteCN.html
4c97d322930491ff8bc6b9f53b133709 *html/segmentationCBS.html
04a3dd249e87f0d5d6094c664d6accd3 *html/segmentationHclust.html
853f7fa69715ecf2c592e940caa4b290 *html/segmentationPSCBS.html
5e0dc475b2299fff17e9f13081ac1109 *html/setMappingBiasVcf.html
3b987917f583ad83a67aa718af774d9a *html/setPriorVcf.html
