d207e3e77f73390142f674c9e70ffe31 *CITATION
3d2eeadc9e645de29f38d74167eafe12 *DESCRIPTION
01e4300c8f7e2f0d146dc415be05fb58 *INDEX
31807d8f3a158183bc1c5865962d5ef7 *Meta/Rd.rds
0df2fe90ee8dad467b0bfc5563be57a5 *Meta/data.rds
f51f28e08b4fc215e2f6955f2c2ae531 *Meta/features.rds
22ee047260aad329bf7c0ba20f1577d7 *Meta/hsearch.rds
b38d1ae0e0ce215d5ea51eb84680dc45 *Meta/links.rds
d3fdfea14b6e5f2a6ea8841177ca4610 *Meta/nsInfo.rds
9fc9edd42791dc483ab4a812e13c5b54 *Meta/package.rds
c7e65a6ed5c3402f217afbc39613a73f *Meta/vignette.rds
34627c1eb27686c3592552b7dec7ff50 *NAMESPACE
da9d2e8bbac2f570a0b1864a688f52c1 *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/PureCN
bebae418bc0df71da0e84bc13b487ad6 *R/PureCN.rdb
a3d6c5e9cbb2325999f198ab5b4f35e0 *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
9df6e3eeaf7b6d8be3a83a84c65516df *doc/PureCN.pdf
523f2584c35f2c61a9801e43ad54fd16 *doc/Quick.R
aed5bfd86a3f914f6b66d427ad85e0b3 *doc/Quick.Rmd
5c7ff35b1371aa240952e3d86c0a7b64 *doc/Quick.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
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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
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9242303d61055871f27ea41c01c1db36 *extdata/example_callable.bed.gz
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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
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efc17f1901c0090230be09f42bd24366 *extdata/test_coverage_overlapping_intervals.txt
c2e77bff4d4fb17d393d49995d86506f *help/AnIndex
d9a68167f142ac4c05c6edc6d19e7231 *help/PureCN.rdb
37e82dfda6663d41128ffedecbdc73e0 *help/PureCN.rdx
5628b331f93ece9935757217e56b77fb *help/aliases.rds
a5dc027a7e90d06d0614c54aff3f5533 *help/paths.rds
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68a44cb17b064c8abfb60785a51ffac4 *html/PureCN-deprecated.html
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845830dc31a31b69e674c1258c66785f *html/annotateTargets.html
1e243201a98cb8ee16b0a3c7e3cca551 *html/bootstrapResults.html
16153412ff15458e81ab79706253df7a *html/calculateBamCoverageByInterval.html
a89e561b5a9d9f01df76146ba4cf65d3 *html/calculateGCContentByInterval.html
d1962ca2640275286fac23f7ccce720d *html/calculateIntervalWeights.html
af9d51b422fd3e05ffbd032afe1d95dd *html/calculateLogRatio.html
8ef2dab790370eacf1c6bdfec2fe084f *html/calculateMappingBiasVcf.html
21bf620d741e91f6eae92c3c09f7067b *html/calculatePowerDetectSomatic.html
13e77a18a86604d2c321f772497bf70c *html/calculateTangentNormal.html
d7cecde7803840658eaad1888b670632 *html/callAlterations.html
54b03822a10f1eb783a46097a068cd1a *html/callAlterationsFromSegmentation.html
adf1dfc2f18f3b43fe7ace128c864b6d *html/callAmplificationsInLowPurity.html
fcfaee2460d11a58d3b1b9d428bcc949 *html/callCIN.html
8fb65725e754671e1b302f60caa6284d *html/callLOH.html
27c42fa0cd4e23d64ce57416aff9f80e *html/callMutationBurden.html
42ab24d993195e1097a3248c6ae8f038 *html/centromeres.html
1a83261ae5d10d82fdec480ae83f82a3 *html/correctCoverageBias.html
eb969994c96afc18202dc81fee92aa86 *html/createCurationFile.html
37d4aab20e5e4efc625b5473133c535b *html/createNormalDatabase.html
67ff62efde81cdb409a62da26c3b2e70 *html/createTargetWeights.html
09b1ade60675fca8c7fdbf89f27579e6 *html/filterIntervals.html
48170ccf6dfe0f66cb4aed5722a7d7b7 *html/filterTargets.html
f0a193400f88a4addbf4afa275ae9bd7 *html/filterVcfBasic.html
5d1c25d408ad21bb30d88127870ab27f *html/filterVcfMuTect.html
3faab5b021ee3bf281cb651b598118c6 *html/filterVcfMuTect2.html
863966fff56c0accb69c4e7513d16f33 *html/findFocal.html
9ac41462625ec533d7866676f61b15d8 *html/getSexFromCoverage.html
ff57c039a0055f50feb154ae783fed6e *html/getSexFromVcf.html
0ef7612856a7b3f4817c796201d975cd *html/plotAbs.html
9d94abe532966b3ebcc4acbd354e9a34 *html/poolCoverage.html
01760a989495d745f3920fcc2b2247b1 *html/predictSomatic.html
f0b13fe191419a9c4dc42144e110a784 *html/preprocessIntervals.html
2d74012a3a3f9d52f61b5774bbf132b4 *html/processMultipleSamples.html
cc3b1f43f91d82b923259b488931a7bc *html/purecn.DNAcopy.bdry.html
21d9c9673d7f8d5ef955e60dd6ecc811 *html/purecn.example.output.html
2b3d99815eb8809461c6a465d1c55109 *html/readCoverageFile.html
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0b6ec5c767d5e2674090521e86795205 *html/readLogRatioFile.html
574a7abefb8a70ebaedc08ca72689d4b *html/readSegmentationFile.html
13a679aee27ea76b2389cb0fcf2a31d3 *html/runAbsoluteCN.html
61597c6de71a64f18763aabb7662bc36 *html/segmentationCBS.html
8f14e10ca1ac7c7b12f0ff06414ccdb6 *html/segmentationHclust.html
9fce235c63d7a5b27f50e25094a791cc *html/segmentationPSCBS.html
76bd6ea5b2c8f2b6767801afba849593 *html/setMappingBiasVcf.html
354df488bdc53b67295bba40d81c2eba *html/setPriorVcf.html
